2021

A. Srivastava, D. Yesudhas, S. Ahmad, M. Michael Gromiha (2021) Deciphering the role of residues involved in disorder-to-order transition regions in archaeal tRNA methyltransferase 5. Genes 12, 399.
S. Akila Parvathy Dharshini, S. Jemimah, Y-h. Taguchi and M. Michael Gromiha (2021) Exploring common therapeutic targets for neurodegenerative disorders using transcriptome study. Front Genet. 12, 639160.
D. Yesudhas, A. Srivastava and M. Michael Gromiha (2021) COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics. Infection. 49, 199–213.
M. Pandey and M. Michael Gromiha (2021) Predicting potential residues associated with lung cancer using deep neural networks. Mutation Res. (in press).
J. Zaucha, M. Heinzinger, A. Kulandaisamy, E. Kataka, Ó.L. Salvádor, P. Popov, B. Rost, M. Michael Gromiha, B.S. Zhorov and D. Frishman (2021) Mutations in transmembrane proteins: diseases, evolutionary insights and prediction. Brief. Bioinf. (in press).
P. Rawat, S. Jemimah, P.K. Ponnuswamy and M. Michael Gromiha (2021) Why are ACE2 binding coronavirus strains SARS-CoV/SARS-CoV-2 wild and NL63 mild? Proteins: Struct Funct Bioinf. 89:389-398.
Y-h. Taguchi, S.A.P. Dharshini and M. Michael Gromiha (2021) Identification of Transcription Factors, Biological Pathways, and Diseases as Mediated by N6-methyladenosine using Tensor Decomposition-Based Unsupervised Feature Extraction. Appl Sci. 11, 213.
R. Prabakaran, P. Rawat, S. Kumar and M. Michael Gromiha (2021) ANuPP: A versatile tool to predict aggregation nucleating regions in peptides and proteins. J Mol Biol. 433, 166707.
R. Nikam, A. Kulandaisamy, K. Harini, D. Sharma and M. Michael Gromiha (2021) ProThermDB: Thermodynamic database for proteins and mutants revisited after 15 years. Nucleic Acids Res. 49, D420-424.
A. Kulandaisamy, R. Sakthivel and M. Michael Gromiha (2021) MPTherm: Database for Membrane Protein Thermodynamics for understanding folding and stability. Brief Bioinf. 22, 2119-2125.
C. Ramakrishnan, R. Nagarajan, M. Sekijima and M. Michael Gromiha (2021). Molecular dynamics simulations of cognate and non-cognate AspRS-tRNA Asp complexes. J Biomol Str Dyn. 39, 493-501.
A. Kulandaisamy, Jan Zaucha, Dmitrij Frishman and M. Michael Gromiha (2021) MPTherm-pred: Analysis and prediction of thermal stability changes upon mutations in transmembrane proteins. J Mol Biol. 433, 166646.
N. Muralidharan, R. Sakthivel, D. Velmurugan and M. Michael Gromiha (2021) Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. J Biomol Struct Dyn. 39, 2673-2678.

2020

M. Michael Gromiha, Editor (2020) Protein Interactions: computational methods, analysis and applications, World Scientific, Singapore.
N.R.S. Shanmugam, J. Blessy, K. Veluraja and M. Michael Gromiha (2020) Prediction of protein-carbohydrate complex binding affinity using structural features. Brief Bioinf. bbaa319.
D. Barh, S. Tiwari, M.E. Weener, V. Azevedo, A. Góes-Neto, M. Michael Gromiha and P. Ghosh (2020) Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comp Biol Med. 126, ​104051.
U. Rangaswamy, S.A.P. Dharshini, D. Yesudhas and M. Michael Gromiha (2020) VEPAD- Predicting the effect of variants associated with Alzheimer’s disease using machine learning. Comp Biol Med. 103933.
A. Shanmugam, N. Muralidharan, D. Velmurugan and M. Michael Gromiha (2020) Therapeutic targets and computational approaches on drug development for COVID-19. Curr Top Med Chem. 20, 2210-20.
S. Sudhakara, C. Ramakrishnan, M. Michael Gromiha and A. Chadha (2020) New insights into the stereospecific reduction by an (S) specific carbonyl reductase from Candida parapsilosis ATCC 7330: Experimental and QM/MM studies. Catal Sci Technol. 10, 5925-34.
S. Jemimah and M. Michael Gromiha (2020) Insights into changes in binding affinity caused by disease mutations in protein-protein complexes. Comp Biol Med. 103829.
S. Jemimah, K. Yugandhar and M. Michael Gromiha (2020) Binding affinity of protein-protein complexes: experimental techniques, databases and computational methods. In “Protein interactions: computational methods, analysis and applications”, (Ed. M.M. Gromiha), World Scientific, Singapore, pp 87-108.
A. Srivastava, D. Yesudhas, A. Kulandaisamy, N. Muralidharan, C. Ramakrishnan, R. Nagarajan and M. Michael Gromiha (2020) Computational approaches for understanding the recognition mechanism of protein–nucleic acid complexes. In “Protein interactions: computational methods, analysis and applications”, (Ed. M.M. Gromiha), World Scientific, Singapore, pp 169-216.
D. Yesudhas, A. Srivastava, N. Muralidharan, A. Kulandaisamy, R. Nagarajan and M. Michael Gromiha (2020) Prediction of nucleic acid binding proteins and their binding sites. In “Protein interactions: computational methods, analysis and applications”, (Ed. M.M. Gromiha), World Scientific, Singapore, pp 217-242.
K. Veluraja, N. R. Siva Shanmugam, J. Jino Blessy, R. A. Jeyaram, B. Lalithamaheswari and M. Michael Gromiha (2020) Protein-carbohydrate complexes: binding site analysis, prediction, binding affinity and molecular dynamics simulations. In “Protein interactions: computational methods, analysis and applications”, (Ed. M.M. Gromiha), World Scientific, Singapore, pp 299-332.
V. Kanakaveti, P. Anoosha, R. Sakthivel, S.K. Rayala and and M. Michael Gromiha (2020) Quantitative structure-activity relationship in ligand-based drug design: concepts and applications. In “Protein interactions: computational methods, analysis and applications”, (Ed. M.M. Gromiha), World Scientific, Singapore, pp 333-349.
N.R.S. Shanmugam, J. Blessy, K. Veluraja and M. Michael Gromiha (2020). ProCaff: protein-carbohydrate complex binding affinity database. Bioinformatics 36(11), 3615-3617.
V.R. Muddapu, S.A.P. Dharshini, V. Srinivasa Chakravarthy and M. Michael Gromiha (2020). Neurodegenerative diseases - Is metabolic deficiency the root cause? Frontiers Neurosci. 14, 213​.
A. Shanmugam, C. Ramakrishnan, D. Velmurugan and M. Michael Gromiha (2020). Identification of potential inhibitors for targets involved in dengue fever. Curr Topics Med Chem. 20, 1738-1756.
A. Srivastava, D. Yesudhas, C. Ramakrishnan, S. Ahmad and M. Michael Gromiha (2020). Role of disordered regions in transferring tyrosine to its cognate tRNA. Int J Biol Macromol. 150:705-713
P. Rawat, R. Prabakaran, R.Sakthivel, A. Mary Thangakani, Sandeep Kumar and M. Michael Gromiha (2020). CPAD 2.0: A repository of curated experimental data on aggregating proteins and peptides. Amyloid 27, 128-133.
V. Kanakaveti, A. Shanmugam, C. Ramakrishnan, P. Anoosha, R. Sakthivel, S.K. Rayala and M. Michael Gromiha (2020). Computational approaches for identifying potential inhibitors on targeting protein interactions in drug discovery. Adv Prot Chem Str Biol. 121, 25-47.
S. Akila Parvathy Dharshini, Y-h. Taguchi and M. Michael Gromiha (2020). Identifying suitable tools for variant detection and differential gene expression using RNA-seq data. Genomics. 112(3):2166-2172..
A. Kulandaisamy, J. Zaucha, R. Sakthivel, D. Frishman and M. Michael Gromiha (2020) Pred-MutHTP: Prediction of disease-causing and neutral mutations in human transmembrane proteins. Human Mutation. 41, 581-590.
S. Jemimah, M. Sekijima and M. Michael Gromiha (2020) ProAffiMuSeq: Sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification. Bioinformatics. 36:1725-1730.
P. Rawat, R. Prabakaran, S. Kumar and M. Michael Gromiha (2020). AggreRATE-Pred: A mathematical model for the prediction of change in aggregation rate upon point mutation. Bioinformatics. 36:1439-1444.
R. A. Jeyaram, C. Anu Radha, M. Michael Gromiha and K. Veluraja (2020). Design of fluorinated sialic acid analog inhibitor to H5 Hemagglutinin of H5N1 Influenza virus through Molecular Dynamics simulation study. J Biomol Str Dyn. 38, 3504-3513​.

2019

R Nikam and M. Michael Gromiha (2019). Seq2Feature: a comprehensive web-based feature extraction tool. Bioinformatics 35:4797-4799.
S. Akila Parvathy Dharshini, Y-h. Taguchi and M. Michael Gromiha (2019) Investigating the energy crisis in Alzheimer disease using transcriptome study. Sci Rep 9, 18509.
S. Chiba, M. Ohue, A. Gryniukova, P. Borysko, S. Zozulya, N. Yasuo, R. Yoshino, K. Ikeda, W-H. Shin, D. Kihara, M. Iwadate, H. Umeyama, T. Ichikawa, R. Teramoto, K-Y. Hsin, V. Gupta, H. Kitano, M. Sakamoto, A. Higuchi, N. Miura, K. Yura, M. Mochizuki, C. Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, I. Nakane, N. Uchida, H. Hakariya, M. Tan, H. Nakamura, S.D. Suzuki, T. Ito, M. Kawatani, K. Kudoh, S. Takashina, K. Yamamoto, Y. Moriwaki, K. Oda, D. Kobayashi, T. Okuno, S. Minami, G. Chikenji, P. Prathipati, C. Nagao, A. Mohsen, M. Ito, K. Mizuguchi, T. Honma, T. Ishida, T. Hirokawa, Y. Akiyama and M. Sekijima (2019) A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Scientific Reports, 9(1), 19585.
A. Sharma, A. Biswas, L. Hongde, S. Sen, P. Anoosha, P. Katsonis, O. Lichtarge, T.C. Dakal, U. Maulik, M. Michael Gromiha, S. Bandyopadhyay, M. Ludwig, F.G. Holz, K.U Loeffler, M.C. Herwig-Carl (2019) Mutational landscape of the BAP1 locus reveals an intrinsic control to regulate the miRNA network and the binding of protein complexes in uveal melanoma. Cancers 11(10), E1600.
P. Parasuraman, J.F.A. Selvin, M. Michael Gromiha , K. Fukui and K. Veluraja (2019). Investigation on the binding specificity of Agrocybe cylindracea galectin towards α(2,6)-linked sialyllactose by molecular modelling and molecular dynamics simulations. J Carb Chem. 38, 566-585
Popov P, Bizin I, A. Kulandaisamy, M. Michael Gromiha and Frishman D(2019). BorodaTM: prediction of disease-associated mutations in membrane proteins with known 3D structure. PLoS ONE, 14(7):e0219452.
P Uma Rani , K VishnuPriya, M.K.N. Sai Varsha, M Nikunj, C Shivam, N Manoj, R Thiagarajan, R Manikandan, M. Michael Gromiha and D Madhulika (2019). Amarogentin, a secoiridoid glycoside, activates AMP-activated protein kinase (AMPK) to exert beneficial vasculo-metabolic effects. BBA - General Subjects 1863:1270-1282.
 
V. Kanakaveti, R. Sakthivel, S.K. Rayala and M. Michael Gromiha (2019). Forging new scaffolds from old: Combining Scaffold hopping and Hierarchical virtual screening for identifying novel Bcl-2 inhibitors. Curr Top Med Chem. 19(13):1162-1172.
 
T. Amemiya, M. Michael Gromiha K. Horimoto and K. Fukui (2019). Drug repositioning for dengue hemorrhagic fever by integrating multiple omics analyses. Sci. Rep. 9, 523.
 
R.A. Jeyaram , T.R.K Priyadarzini , C. Anu Radha , N.R. Siva Shanmugam , C. Ramakrishnan , M. Michael Gromiha and K. Veluraja (2019). Molecular dynamics simulation studies on influenza A virus H5N1 complexed with sialic acid and fluorinated sialic acid. J Biomol Struct Dyn. 37(18):4813-4824.
 
A. Kulandaisamy, S. Binny Priya, R. Sakthivel, Dmitrij Frishman and M. Michael Gromiha(2019). Statistical analysis of disease-causing and neutral mutations in human membrane proteins. PROTEINS 87, 452-466.
 
K. Ganesan, A. Kulandaisamy,S. Binny Priya, and M. Michael Gromiha(2019). HuVarBase: A human variant database with comprehensive information at gene and protein levels. PLoS ONE 14(1), e0210475.
 
M. Michael Gromiha, R. Nagarajan and S. Selvaraj (2019). Protein structural bioinformatics: an overview. Encyc Bioinf Comp Biol. 2, 445-459. INVITED REVIEW.
 
V. Kanakaveti, P. Anoosha, R. Sakthivel, S. K. Rayala and M. Michael Gromiha (2019). Influence of amino acid mutations and small molecules for targeted inhibition of proteins involved in cancer. Curr Top Med Chem. 19, 457-466.
 
S. Akila Parvathy Dharshini, Y-h. Taguchi and M. Michael Gromiha(2019). Exploring the selective vulnerability in Alzheimer disease using tissue specific variant analysis. Genomics. 111, 936-949
 
S. Binny Priya and M. Michael Gromiha (2019). Structural insights into the aggregation mechanism of huntingtin exon 1 protein fragment with different polyQ-lengths. J Cell Biochem. 120, 10519-10529.
 
S. Anusuya, M. Michael Gromiha (2019). Structural basis of flavonoids as dengue polymerase inhibitors: Insights from QSAR and docking studies. J Biomol Struct Dyn. 37:104-115.
 

2018

P. Rawat, S. Kumar and M. Michael Gromiha(2018). An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins. Int J Biol Macromol. 118, 1157-1167.
 
D-S. Huang, M. Michael Gromiha, K. Han A. Hussain (Editors) Lecture Notes in Artificial Intelligence(2018). Springer, Heidelberg, Vol. 10956.
 
A. Kumaraswamy, A. Mamidi, P. Desai, A. Sivagnanam, L.R. Perumalsamy, C. Ramakrishnan, M. Michael Gromiha K. Rajalingam and S. Mahalingam (2018). The non-enzymatic RAS effector RASSF7 inhibits oncogenic c-Myc function. J Biol Chem. 293(40),15691-15705.
 
D-S. Huang , V. Bevilacqua and M. Michael Gromiha(2018). Guest Editorial for Special Section on the 12th International Conference on Intelligent Computing (ICIC) IEEE/ACM Trans Comput Biol Bioinform. 15(5),1433-1435.
 
A. Srivastava, S. Ahmad and M. Michael Gromiha(2018). Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. Int J Mol Sci. 19(6), 1595.
 
N.R. Siva Shanmugam, J. Fermin Angelo Selvin, K. Veluraja and M. Michael Gromiha. Identification and analysis of key residues involved in folding and binding of protein-carbohydrate complexes. Protein Pept Lett. 25(4),379-389.
 
S. Jemimah, M. Michael Gromiha (2018). Exploring additivity effects of double mutations on the binding affinity of protein-protein complexes. Proteins. 86(5), 536-547.
 
A. Kulandaisamy, S. Binny Priya, R. Sakthivel, S. Tarnovskaya, I. Bizin, P. Hönigschmid, D. Frishman and M. M. Gromiha (2018). MutHTP: Mutations in Human Transmembrane Proteins. Bioinformatics. 34(13), 2325-2326.
 
C. Ramakrishnan, A. M. Thangakani, D. Velmurugan, D. A. Krishnan, M. Sekijima, Y. Akiyama and M. Michael Gromiha (2018). Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques. J Biomol Struct Dyn.36(6), 1566-1576.
 
A. Kulandaisamy, A. Srivastava,R. Nagarajan and M. Michael Gromiha (2018). Dissecting and analyzing key residues in protein-DNA complexes. J Mol Recog. 31(4).
 
A. Kulandaisamy, A. Srivastava, P. Kumar, R. Nagarajan, S. Binny Priya and M. Michael Gromiha (2018).Identification and analysis of key residues in protein-RNA complexes. IEEE/ACM Trans Comput Biol Bioinform. 15(5), 1436-1444.
 

2017

M. Michael Gromiha, K. Yugandhar, and S. Jemimah (2017) Protein-protein interactions: scoring schemes and binding affinity. Curr Opin Struct Biol., 44, 31-38.
 
P. Anoosha, R. Sakthivel, M. Michael Gromiha (2017). Investigating mutation-specific biological activities of small molecules using quantitative structure-activity relationship for epidermal growth factor receptor in cancer. Mutat Res. , 806, 19-26.
 
S. Chiba, T. Ishida, K. Ikeda, M. Mochizuki, R. Teramoto, Y-h Taguchi, M. Iwadate, H. Umeyama, C. Ramakrishnan, A. M. Thangakani, D. Velmurugan, M. Michael Gromiha, T. Okuno, K. Kato, S. Minami, G. Chikenji, S.D. Suzuki, K. Yanagisawa, W.H. Shin, D. Kihara, K. Yamamoto, Y. Moriwaki, N. Yasuo, R. Yoshino, S. Zozulya, P. Borysko, R. Stavniichuk, T. Honma, T. Hirokawa, Y. Akiyama, M. Sekijima (2017). An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes. Sci Rep.,7(1):12038.
 
S. Jemimah, K. Yugandhar, M. Michael Gromiha (2017). PROXiMATE: a database of mutant protein–protein complex thermodynamics and kinetics. Bioinformatics, 33(17), 2787-2788.
 
S. D. Huang, A. Hussain,,K. Han,M. Michael Gromiha (Editors) Lecture Notes in Artificial Intelligence(2017), Springer, Heidelberg, Vol. 1036.
 
R. Prabakaran, D. Goel, S. Kumar and M. Michael Gromiha (2017) Aggregation prone regions in human proteome: Insights from large-scale data analyses. Proteins, 85(6):1099-1118.
 
M. Michael Gromiha and K. Yugandhar (2017) Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes. Prog Biophys Mol Biol. , 128, 33-38.
 
V. Kanakaveti, R. Sakthivel, Suresh K. Rayala and M. Michael Gromiha (2017) Importance of functional groups in predicting the activity of small molecule inhibitors of Bcl-2 and Bcl-xL. Chem Biol Drug Des., 90, 308-316.
 
A. Kulandaisamy, V. Lathi, K. ViswaPoorani, K. Yugandhar, and M. Michael Gromiha (2017) Important amino acid residues involved in folding and binding of protein-protein complexes. Int J Biol Macromol., 94 (Pt A), 438-444.
 
K. Yugandhar and M. Michael Gromiha (2017) Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes. Methods Mol Biol., 1484, 237-253.
 
S. Anusuya and M. Michael Gromiha (2017) Quercetin derivatives as non-nucleoside inhibitors for dengue polymerase: molecular docking, molecular dynamics simulation and binding free energy calculation, J Biomol Struct Dyn., 35, 2895-2909 .
 
S. Anusuya, M. Kesherwani, K. Vishnupriya, A. Vimala, G. Shanmugam, D. Velmurugan and M. Michael Gromiha (2017) Drug-Target Interactions: Prediction Methods and Applications. Curr Protein Pept Sci., 18, 1-25.
 
M. Kesherwani, M. Michael Gromiha, K. Fukui and D. Velmurugan (2017) Identification of novel natural inhibitor for NorM -A Multidrug and Toxic compound extrusion Transporter-An in silico molecular modeling and simulation studies. J Biomol Struct Dyn., 35, 58-77.
 

2016

P. Chaudhary, A. N. Naganathan, M. Michael Gromiha (2016) Prediction of change in protein unfolding rates upon point mutations in two state proteins. Biochim Biophys Acta. 1864(9), 1104-1109.
 
D-S. Huang, V. Bevilacqua, and M. Michael Gromiha (2016) Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC). IEEE Trans. Comp. Biol. Bioinf., 13, 1-3.
 
S. Muthusamy, M. Prakash, C. Ramakrishnan, M. Michael Gromiha and V. Kesavan (2016) Organocatalytic Enantioselective Assembly of Spirooxindole-naphthopyrans through Tandem Friedel-Crafts Type/Hemiketalization. ChemCatChem, 8, 1708-1712.
 
R. Nagarajan and M. Michael Gromiha (2016) Computational Analysis of SimilarProtein-DNA Complexes from Different Organisms to Understand Organism Specific Recognition. Lect. Notes Comp. Sci., 9772, 888-894.
 
E. L. Folador, P. V. S. D. de Carvalho, W. M. Silva, R. S. Ferreira, A. Silva, M. Michael Gromiha, P. Ghosh, D. Barh, V. Azevedo, and R. Rottger (2016) In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. BMC Systems Biology, 1, 103.
 
K. Yugandhar and M. Michael Gromiha (2016) Analysis of protein-protein interaction networks based on binding affinity. Current Protein & Peptide Science, 17(1): 72-81.
 
S. Anusuya, D. Velmurugan and M. Michael Gromiha (2016) Identification of Dengue Viral RNA Dependent RNA Polymerase Inhibitor using Computational Fragment Based Approaches and Molecular Dynamics Study. Journal of Biomolecular Structure and Dynamics, 34(7), 1512-32.
 
R. Nagarajan, A. Archana, A. Mary Thangakani, S. Jemimah, D. Velmurugan and M. Michael Gromiha (2016) PDBparam: Online Resource for Computing Structural Parameters of Proteins. Bioinformatics and Biology Insights, 10, 73-80.
 
C. Magyar, M. Michael Gromiha, Z. Savoly, and I. Simon (2016) The role of stabilization centers in protein thermal stability. Biochemical and biophysical research communications, 471(1), 57-62.
 
M. Michael Gromiha, P. Anoosha, and Liang-Tsung Huang (2016) Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants. Methods Mol Biol., 1415, 71-89.
 
A. Mary Thangakani, R. Nagarajan, S. Kumar, R. Sakthivel, D. Velmurugan and M. Michael Gromiha* (2016) CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PLoS One, 11(4), e0152949.
 
S. Kumar, A. Mary Thangakani, R. Nagarajan, Satish K. Singh, D. Velmurugan and M. Michael Gromiha* (2016) Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions. Scientific Reports, 6, 22258.
 
D. R. Tompa, M. Michael Gromiha and K. Saraboji* (2016) Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins. J. Mol. Graph. Model, 64, 85-93.
 
P. Anoosha, R. Sakthivel, M. Michael Gromiha*(2016) Exploring preferred amino acid mutations in cancer genes: Applications to identify potential drug targets. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1862(2), 155-165
 
N. Saranya, KM Saravanan, M. Michael Gromiha, S. Selvaraj* (2016) Analysis of secondary structural and physico-chemical changes in protein-protein complexes. J Biomol Struct Dyn., 34(3):508-16.
 

2015

P. Anoosha, Liang-Tsung Huang, R. Sakthivel, D. Karunagaran, M. Michael Gromiha*(2015) Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer.Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 780, 24-34.
 
R. Nagarajan, Sonia P Chothani, C. Ramakrishnan, M. Sekijima, M. Michael Gromiha* (2015) Structure based approach for understanding organism specific recognition of protein-RNA complexes, Biology Direct, 10:8.
 
Priyashree Chaudhary, Athi N. Naganathan, M. Michael Gromiha* (2015) Folding RaCe: A Robust Method for Predicting Changes in Protein Folding Rates upon Point Mutations. Bioinformatics, 31(13), 2091-2097.
 
S. Kumar, R.H. Robins, P.M. Buck, T.P. Hickling, A. M. Thangakani, L. Li, S. K. Singh, M Michael Gromiha (2015) Biopharmaceutical Informatics: Applications of Computation in Biologic Drug Development. In "Developability of Biotherapeutics" (Eds) S. Kumar and S.K. Singh, CRC Press, New York, pp 3-34.
 
Veeramani Murugan, Ponnusamy Parasuraman, Jeyasigamani FA Selvin, Thanu RK Priyadarzini, M Michael Gromiha, Kazuhiko Fukui, Kasinadar Veluraja* (2015) Geometry Optimization of Carbohydrate Binding Sites of Influenza: A Quantum Mechanical Approach.Journal of Carbohydrate Chemistry, 34(7), 409-429.
 
Ponnusamy Parasuraman, Veeramani Murugan, Jeyasigamani FA Selvin, M Michael Gromiha, Kazuhiko Fukui, Kasinadar Veluraja* (2015) Theoretical investigation on the glycan-binding specificity of Agrocybe cylindracea galectin using molecular modeling and molecular dynamics simulation studies.Journal of Molecular Recognition, 28(9), 528–538
 
Huntaro Chiba, Kazuyoshi Ikeda, Takashi Ishida, M. Michael Gromiha, Y-h Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Kun-Yi Hsin, Hiroaki Kitano, Kazuki Yamamoto, Nobuyoshi Sugaya, Koya Kato, Tatsuya Okuno, George Chikenji, Masahiro Mochizuki, Nobuaki Yasuo, Ryunosuke Yoshino, Keisuke Yanagisawa, Tomohiro Ban, Reiji Teramoto, C. Ramakrishnan, A. Mary Thangakani, D Velmurugan, Philip Prathipati, Junichi Ito, Yuko Tsuchiya, Kenji Mizuguchi, Teruki Honma, Takatsugu Hirokawa , Yutaka Akiyama* (2015) Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target. Scientific Reports, 5, 17209.
 
P. Anoosha, R. Sakthivel, M. Michael Gromiha*(2015) Prediction of protein disorder upon amino acid substitutions, Analytical Biochemistry, 491, 18-22
 
S. Anandakumar, S. Vijayakumar, N. Arumugam, M Michael Gromiha (2015) Mammalian Mitochondrial ncRNA Database. Bioinformation 11, 512-513.
 
A. Vimala*, C. Ramakrishnan, M. Michael Gromiha* (2015) Identifying a potential receptor for the antibacterial peptide of sponge Axinella donnani endosymbiont. Gene, 566(2), 166-174.
 
M. Xavier Suresh, M. Michael Gromiha, Makiko Suwa (2015) Development of a Machine Learning Method to Predict Membrane Protein-Ligand Binding Residues Using Basic Sequence Information. Advances in Bioinformatics, 1-7
 
M. Michael Gromiha*, P. Anoosha, D. Velmurugan, K. Fukui (2015) Mutational studies to understand the structure-function relationship in multidrug efflux transporters: application for distinguishing mutants with high specificity. International Journal of Biological Macromolecules,75, 218-224.
 

2014

K. Yugandhar and M. Michael Gromiha* (2014) Protein-protein binding affinity prediction from amino acid sequence. Bioinformatics, 30(24), 3583-9
 
K. Yugandhar and M. Michael Gromiha* (2014) Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches. Proteins, 82(9), 2088-2096.
 
M. Michael Gromiha* (2014) Editorial: structure and function of proteins. Protein & Peptide Letters, 21(8), 705-706.
 
C. Ramakrishnan, A. M. Thangakani, D. Velmurugan, M. Michael Gromiha* (2014) Identification of Novel c-Yes Kinase Inhibitors. Lecture Notes in Computer Science, 8590, 494-500.
 
M. Michael Gromiha*, K. Veluraja and Kazuhiko Fukui (2014) Identification and Analysis of Binding Site Residues in Protein-carbohydrate Complexes using Energy Based Approach. Protein & Peptide Letters, 21(8), 799-807.
 
A. Mary Thangakani, Sandeep Kumar, R. Nagarajan, D. Velmurugan and M. Michael Gromiha* (2014) GAP: Towards almost hundred percent prediction for β-strand mediated aggregating peptides with distinct morphologies. Bioinformatics, 30(14), 1983-1990.
 
Liang-Tsung Huang* , Chao-Chin Wu , Lien-Fu Lai , M. Michael Gromiha , Chang-Sheng Wang and Yet-Ran Chen (2014) Data Mining Application in Biomedical Informatics for Probing into Protein Stability upon Double Mutation. Applied Mathematics and Information Sciences, 8, 125-132.
 
B. Nagarathnam, Snehal D. Karpe, K. Harini, K. Sankar, M. Iftekhar, D. Rajesh, S. Giji, G. Archunan, V. Balakrishnan, M. Michael Gromiha, W. Nemoto, K. Fukui and R. Sowdhamini (2014) DOR – a Database of Olfactory Receptors – Integrated Repository for Sequence and Secondary Structural Information of Olfactory Receptors in Selected Eukaryotic Genomes. Bioinformatics and Biology Insights, 8, 147-158.
 
P Parasuraman, V Murugan, Jeyasigamani F. A. Selvin,M. Michael Gromiha, K Fukui and K Veluraja* (2014) Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations. Journal of Molecular Recognition, 27, 482-492.
 
R. Nagarajan and M. Michael Gromiha* (2014) Prediction of RNA binding residues: An extensive analysis based on structure and function to select the best predictor. PLoS One, 9(3), e91140.
 
M. Michael Gromiha and Y-Y. Ou (2014) Bioinformatics approaches for functional annotation of membrane proteins. Brief. Bioinf, 15(2), 155-168.

2013

R. Nagarajan, Shandar Ahmad and M. Michael Gromiha* (2013) Novel approach for selecting the best predictor for identifying binding sites in DNA binding proteins. Nucleic Acids Res., 41(16), 7606-7614.
 
M. Michael Gromiha* M.C. Pathak, K. Saraboji, E. Ortlund and E. Gaucher (2013) Hydrophobic environment is a key factor for the stability of thermophilic proteins. PROTEINS: Struct. Funct. Bioinf. 81:715-21.
 
A.M. Thangakani, S. Kumar, D. Velmurugan and M. Michael Gromiha,* (2013) Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β- aggregate forming peptide sequences. BMC Bioinformatics. 14(Suppl 8), S6
 
Y-Y. Ou, S-A. Chen, Y-M. Chang, D. Velmurugan, K. Fukui and M. Michael Gromiha* (2013) Classification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties. PROTEINS: Struct. Funct. Bioinf., 81(9), 1634-43
 
M. Michael Gromiha (2013) Computational approaches for understanding the recognition mechanism of protein complexes. In "Biomolecular forms and functions", (Ed. M. Bansal and N. Srinivasan), IISc Press and Word Scientific, Singapore, pp 198-209.
 
M. Michael Gromiha and R. Nagarajan (2013) Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. Adv. Protein Chem. Str. Biol., 91, 65-99.

2012

 
M.Michael Gromiha A.M. Thangakani, S. Kumar and D. Velmurugan (2012) Sequence analysis and discrimination of amyloid and non-amyloid peptides. Comm. Comp. Inf. Sci. 304, 447-452.
 
Priyadarzini TR, Selvin JF, Gromiha MM, Fukui K, Veluraja K. (2012) Theoretical investigation on the binding specificity of sialyldisaccharides with Hemagglutinins of Influenza A virus by MD simulations. J. Biol. Chem. 287:34547-57.
 
Gromiha MM*, Huang DS. (2012) Introduction: advanced intelligent computing theories and their applications in bioinformatics. BMC Bioinformatics. 13 (Suppl 7): I1.
 
Gromiha MM*, Harini K, Sowdhamini R, Fukui K. (2012) Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity. BMC Bioinformatics.13 (Suppl 7): S1.
 
Huang LT, Gromiha MM*. (2012) Real value prediction of protein folding rate change upon point mutation. J Comput Aided Mol Des. 26:339-47.
 
M. Michael Gromiha* (2012) Editorial: Bioinformatics on Proteins and Complexes. Current Bioinformatics 7, 109-110.
 
M. Michael Gromiha* (2012) Development of RNA Stiffness Parameters and Analysis on Protein-RNA Binding Specificity: Comparison with DNA. Current Bioinformatics 7, 173-179
 
C-C. Wu, L-F. Lai, M. Michael Gromiha, L-T. Huang (2012) High throughput computing for the prediction of protein stability change upon mutation using a knowledge-based approach. Int. J. Data Mining and Bioinf. (in press).
 
A.M. Thangakani, S. Kumar, D. Velmurugan and M.M. Gromiha* (2012) How do thermophilic proteins resist aggregation? PROTEINS: Structure, Function and Bioinformatics, 80:1003-15.
 
Singh H, Chauhan JS, Gromiha MM Open Source Drug Discovery Consortium, Raghava GP. (2012) ccPDB: compilation and creation of data sets from Protein Data Bank. Nucleic Acids Res. 40(Database issue):D486-9.
 

2011

Gromiha MM, Saranya N, Selvaraj S, Jayaram B, Fukui K. (2011) Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes. Proteome Sci. 9; :S13.
 
Chen SA, Ou YY, Lee TY, Gromiha MM* (2011) Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. Bioinformatics. 27(15):2062-7.
 
Gromiha MM and Huang LT. (2011) Machine Learning Algorithms for Predicting Protein Folding Rates and Stability of Mutant Proteins: Comparison with Statistical Method. Curr Protein Pept Sci. 2011 Sep 1;12(6):490-502.
 
M. M. Gromiha, R. Sowdhamini, K. Fukui, Structure-Function Relationship in Olfactory Receptors, Lecture Notes in Bioinformatics, 6840, 618-623.
 
M. Michael Gromiha* and K. Fukui (2011) Scoring function based approach for understanding the recognition mechanism of protein-DNA complexes. J Chem Inf Model. Mar 28;51(3):721-9.
 
K. Imai, N. Fujita, M. Michael Gromiha and P. Horton (2011) Eukaryote-wide sequence analysis of mitochondrial beta-barrel outer membrane proteins. BMC Genomics. 12:79.
 
M. Michael Gromiha * (2011) Influence of long-range contacts and surrounding residues to the transition state structures of proteins. Anal. Biochem. 408, 32-36.
 
M. Kumar, M. Michael Gromiha and G.P.S. Raghava (2011) SVM based prediction of RNA-binding proteins using binding residues and evolutionary information. J. Mol. Recogn. J. Mol. Recogn. 24:303-13.
 

2010

M. Michael Gromiha (2010). Protein Bioinformatics: From Sequence to Function. Elsevier Publishers
 
J. Song, K. Takemoto, H. Shen, H. Tan, M. Michael Gromiha (2010). and T. Akutsu (2010) Prediction of protein folding rates from structural topology and complex network properties. ISPJ Trans. Bioinf. 3, 40-53.
 
M. Michael Gromiha (2010) Protein folding, stability and interactions. Curr. Prot. Pept. Sci. 11, 497 (Editorial).
 
S-A. Chen, Y-Y. Ou and M. Michael Gromiha (2010). Topology prediction of α-helical and β-barrel transmembrane proteins using RBF networks. Lecture Notes in Comp. Sci. 6215, 642-649 (BEST PAPER AWARD).
 
M. Michael Gromiha * (2010)., K. Yokota and K. Fukui (2010) Understanding the recognition mechanism of protein-RNA complexes using energy based approach. Curr. Protein Peptide Sci. 11, 629-638 (COVER PAGE).
 
L-T. Huang, L-F. Lai and M. Michael Gromiha (2010). Human-readable rule generator for integrating amino acid sequence information and stability of mutant proteins. IEEE ACM Trans. Comp. Biol. Bioinf. 7, 681-687.
 
M. Michael Gromiha and A. Sarai (2010). Thermodynamic database for proteins: features and applications. Methods Mol. Biol. 609, 97-112.
 
Y-Y. Ou, S.A. Chen and M. Michael Gromiha (2010). Classification of transporters using efficient radial basis function networks with position-specific scoring matrices and biochemical properties. PROTEINS: Struct. Funct. Bioinf. 78, 1789-1797.
 
M. Michael Gromiha, K. Yokota and K. Fukui (2010). Sequence and structural analysis of binding site residues in protein-protein complexes. Int. J. Biol. Macromol. 46, 187-192.
 
Y-Y. Ou, S.A. Chen and M. Michael Gromiha (2010). Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy. J. Comp. Chem. 13, 217-223
 
L-T. Huang, L-F. Lai, C-C. Wu and M. Michael Gromiha (2010). Development of knowledge based system for predicting the stability of proteins upon point mutations. Neurocomputing 73, 2293-2299.
 
M. Michael Gromiha, S. Selvaraj, B. Jayaram and K. Fukui (2010). Identification and analysis of binding site residues in protein complexes: energy based approach. Lecture Notes in Comp. Sci. 6215, 626-633.
 
S. Kumar, S. Singh and M. Michael Gromiha (2010). Temperature Dependent Molecular Adaptations in Microbial Proteins. Wiley Encyclopedia of Industrial Biotechnology 7, 4647-4661.
 
L-T. Huang and M. Michael Gromiha (2010). First insight into the prediction of protein folding rate upon mutation. Bioinformatics 26, 2121-2127.
 

2009

M. Michael Gromiha, Y. Yabuki, M.X. Suresh, A.M. Thangakani, M. Suwa and K. Fukui K. (2009). TMFunction: database for functional residues in membrane proteins. Nucl. Acids Res. 37, D201-204.
 
M. Michael Gromiha and S. Selvaraj (2009). Proteins: computational analysis of structure, function and stability. Wiley Encyclopedia on Chemical Biology 4, 174-182. INVITED REVIEW
 
M. Michael Gromiha (2009). Multiple contact network is a key determinant to protein folding rates. J. Chem. Inf. Model. 49, 1130-1135.
 
L-T. Huang and M. Michael Gromiha (2009). Reliable Prediction of Protein Thermostability Change upon Double Mutation from Amino Acid Sequence. Bioinformatics 25, 2181-2187.
 
M. Michael Gromiha (2009). Revisiting "reverse hydrophobic effect": applicable only to coil mutations at the surface. Biopolymers 91, 591-599.
 
M. Michael Gromiha (2009). Intrinsic Relationship of Amino Acid Composition/Occurrence with Topological Parameters and Protein Folding Rates. Open Str. Biol. J. 3, 126-142.
 
M. Michael Gromiha, K. Yokota and K. Fukui (2009). Energy based approach for understanding the recognition mechanism of protein-protein complexes. Mol. Biosyst. 5, 1779-1786.
 

2008

K. Imai, M. Michael Gromiha and P. Horton (2008). Mitochondrial beta-Barrel Proteins, an Exclusive Club? CELL 135, 1158-1159.
 
M. Michael Gromiha and S. Selvaraj (2008). Bioinformatics Approaches for Understanding and Predicting Protein Folding Rates. Current Bioinformatics 3, 1-9. INVITED REVIEW
 
L-T. Huang and M. Michael Gromiha (2008). Analysis and prediction of protein folding rates using quadratic response surface models. J. Comp. Chem. 29, 1675-1683.
 
C. Motono, M. Michael Gromiha and S. Kumar (2008). Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis. PROTEINS: Struct. Funct. Bioinf. 71, 655-669.
 
M. Michael Gromiha , L-T. Huang and L-F. Lai (2008). Sequence Based Prediction of Protein Mutant Stability and Discrimination of Thermophilic Proteins. Lect. Notes Bioinf. 5265, 1-12.
 
A.Y. Istomin, M. Michael Gromiha, O.K. Vorov, D.J. Jacobs and D.R. Livesay (2008) New insight into long-range nonadditivity within protein double-mutant cycles. PROTEINS: Struct. Funct. Bioinf. 70, 915-924.
 
R.L. Martis, S.K. Singh, M. Michael Gromiha, and C. Santhosh (2008) Role of cation-pi interactions in single chain 'all-alpha' proteins. J. Theor. Biol. 250, 655-662.
 
M. Michael Gromiha and M.X. Suresh (2008) Discrimination of mesophilic and thermophilic proteins using machine learning algorithms. PROTEINS: Struct. Funct. Bioinf. 70, 1274-1279.
 
Y-Y. Ou, M. Michael Gromiha, S-A. Chen and M. Suwa (2008). TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles. Comp. Biol. Chem. 32, 227-231.
 
M. Kumar, M. Michael Gromiha and G.P.S. Raghava (2008). Prediction of RNA binding sites in a protein using SVM and PSSM profile. PROTEINS: Struct. Funct. Bioinf. 71, 189-194.
 
M. Michael Gromiha and Y. Yabuki (2008). Functional discrimination of membrane proteins using machine learning techniques. BMC Bioinformatics 9, 135.
 

2007

M. Michael Gromiha, Y. Yabuki, S. Kundu, S. Suharnan and M. Suwa (2007). TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res. 35, D314-316.
 
V. Parthiban, M. Michael Gromiha, C. Hoppe and D. Schomburg (2007). Structural analysis and prediction of protein mutant stability using distance and torsion potentials: Role of secondary structure and solvent accessibility. PROTEINS: Struct. Funct. Bioinf. 66, 41-52.
 
L-T. Huang, K. Saraboji, S-Y. Ho, S-F. Hwang. M.N. Ponnuswamy and M. Michael Gromiha (2007). Prediction of protein mutant stability using classification and regression tool. Biophys. Chem. 125, 462-470.
 
M. Michael Gromiha, Y. Yabuki and M. Suwa (2007). TMB Finding Pipeline: Novel Approach for Detecting Beta-barrel Membrane Proteins in Genomic Sequences. J. Chem. Inf. Model. 47, 2456-2461.
 
L-T. Huang, M. Michael Gromiha and S-Y. Ho (2007). iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics 23, 1292-1293.
 
V. Parthiban V, M. Michael Gromiha, M. Abhinandan and D. Schomburg (2007). Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development. BMC Struct. Biol. 7, 54.
 
L-T. Huang, M. Michael Gromiha and S-Y. Ho (2007). Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model. J. Mol. Model. 13, 879-890.
 
M. Michael Gromiha and M. Suwa (2007). Current developments on beta-barrel membrane proteins: sequence and structural analysis, discrimination and prediction. Curr. Prot. Pept. Sci. 8, 580-599. INVITED REVIEW
 
Y-h. Taguchi and M. Michael Gromiha (2007). Application of amino acid occurrence for discriminating different folding types of globular proteins. BMC Bioinformatics 8, 404.
 
M. Kumar, M. Michael Gromiha and G.P.S. Raghava(2007). Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 8, 463.
 
M. Michael Gromiha (2007). Prediction of protein stability upon point mutations. Biochem. Soc. Trans. 35, 1569-1573.
 

2006

M. Michael Gromiha and M. Suwa (2006). Discrimination of Outer Membrane Proteins using Machine Learning Algorithms. PROTEINS: Struct. Funct. Bioinf. 63, 1031-1037.
 
S. Chakkaravarthi and M. Michael Gromiha (2006). Analysis of Cation-pi Interactions to the Structural Stability of RNA Binding Proteins. Polymer 47, 709-721.
 
M.D.S. Kumar, K. Bava, M. Michael Gromiha, P. Prabakaran, K. Kitajima, H. Uedaira and A. Sarai (2006). ProTherm and ProNIT: Thermodynamic Databases for Proteins and Protein-Nucleic Acid Interactions Nucl. Acids Res. 34, D204-206.
 
M. Michael Gromiha and S. Selvaraj (2006). Salient Features of Residue Contacts in Protein Structures for Determining their Folding and Stability. In "Protein Folding: New Research", Nova Science Publishers, New York, USA, pp 249-265. INVITED REVIEW
 
K. Saraboji, M. Michael Gromiha and M.N. Ponnuswamy (2006). Average assignment method for predicting the stability of protein mutants. Biopolymers 82, 80-92.
 
M.D.S. Kumar and M. Michael Gromiha (2006). PINT: Protein-protein Interactions Thermodynamic Database Nucl. Acids Res. 34, D195-198.
 
M. Michael Gromiha , S. Selvaraj and A. Mary Thangakani (2006). A Statistical Method for Predicting Protein Unfolding Rates from Amino Acid Sequence. J. Chem. Inf. Model 46, 1503-1508.
 
V. Parthiban, M. Michael Gromiha and D. Schomburg (2006). CUPSAT: Prediction of Protein Stability upon Point Mutations. Nucleic Acid Res. 34, W239-242.
 
Y.H. Singh, M. Michael Gromiha, A. Sarai and S. Ahmad (2006) Atom-wise Statistics and Prediction of Solvent Accessibility in Proteins. Biophys. Chem. 124, 145-154.
 
S. Chakkaravarthi, M.M. Babu, M. Michael Gromiha, G. Jayaraman and R. Sethumadhavan, (2006) Exploring the environmental preference of weak interactions in (a/b)8 barrel proteins. PROTEINS: Struct. Funct. Bioinf. 65, 75-86.
 
M. Michael Gromiha and M. Suwa (2006). Influence of amino acid properties for discriminating outer membrane proteins at better accuracy. Biochim Biophys Acta. 1764, 1493-1497.
 
P. Prabakaran, J.G. Siebers, S. Ahmad, M. Michael Gromiha, M.G. Singarayan and A. Sarai (2006) Classification of Protein-DNA complexes Based on Structural Descriptors. Structure 14, 1355-1367.
 
M.N. Ponnuswamy, M. Michael Gromiha, S.M.M. Sony and K. Saraboji (2006) Conformational aspects and interaction studies of heterocyclic drugs. In "Topics in Heterocyclic Chemistry" (Ed. G.P. Gupta), Springer-Verlag Publishers, Heidelberg, pp 81-147. INVITED REVIEW
 
L.T. Huang, M. Michael Gromiha, S.F. Hwang SF and S.Y. (2006). Knowledge acquisition and development of accurate rules for predicting protein stability changes. Comput Biol Chem. 30, 408-415.
 
M. Michael Gromiha, A.M. Thangakani and S. Selvaraj (2006). FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acid Res. 34, W70-74.

2005

M. Michael Gromiha and M. Suwa (2005). A Simple Statistical Method for Discriminating Outer Membrane Proteins with Better Accuracy. Bioinformatics 21, 961-968.
 
M. Michael Gromiha (2005). Distinct Roles of Conventional Non-covalent and Cation-pi Interactions in Protein Stability. Polymer 46, 983-990.
 
K. Saraboji, M. Michael Gromiha and M.N. Ponnuswamy (2005). Relative Importance of Secondary Structure and Solvent Accessibility to the Stability of Protein Mutants: A Case Study with Amino Acid Properties and Energetics on T4 and Human Lysozymes. Comp. Biol. Chem. 29, 25-35.
 
M. Michael Gromiha and S. Ahmad (2005). Role of Solvent Accessibility in Structure Based Drug Design. Current Computer Aided Drug Design 1, 223-235. INVITED REVIEW
 
M. Michael Gromiha (2005) Motifs in outer membrane protein sequences: applications for discrimination. Biophys. Chem. 117, 65-71.
 
M. Michael Gromiha and M. Suwa (2005). Structural Analysis of Residues Involving Cation-pi Interactions in Different Folding Types of Membrane Proteins. Int. J. Biol. Macromol. 35, 55-62.
 
A. Sarai, J. Siebers, S. Selvaraj, M. Michael Gromiha and H. Kono (2005). Integration of Bioinformatics and Computational Biology to Understand Protein-DNA Recognition Mechanism. J. Bioinf. Comput. Biol. 3, 169-183.
 
M. Michael Gromiha (2005). A Statistical Model for Predicting Protein Folding Rates from Amino Acid Sequence with Structural Class Information. J. Chem. Inf. Model. 45, 494-501.
 
K. Saraboji, M. Michael Gromiha and M.N. Ponnuswamy (2005). Importance of Main-chain Hydrophobic Free Energy to the Stability of Thermophilic Proteins. Int. J. Biol. Macromol. 35, 211-220.
 
M. Michael Gromiha, S. Ahmad and M. Suwa (2005) Application of residue distribution along the sequence for discriminating outer membrane proteins. Comp. Biol. Chem. 29, 135-142.
 
C. Magyar, M. Michael Gromiha, G. Pujadas, G.E. Tusnady and I. Simon (2005) SRide: a Server for Identifying Stabilizing Residues in Proteins. Nucleic Acids Res. 33, W303-305.
 
M. Michael Gromiha (2005). Influence of DNA Stiffness in Protein-DNA Recognition. J. Biotech. 117, 137-145.
 
K.J. Park, M. Michael Gromiha, P. Horton and M. Suwa (2005) Discrimination of outer membrane proteins using support vector machines. Bioinformatics 21, 4223-4229.
 
M. Michael Gromiha, J.G. Siebers, S. Selvaraj, H. Kono and A. Sarai (2005). Role of inter and intramolecular interactions in protein-DNA recognition. GENE 364, 108-113. (INVITED REVIEW)
 
M. Michael Gromiha, S. Ahmad and M. Suwa (2005) TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res. 33, W164-167.
 

2004

M. Michael Gromiha and S. Selvaraj (2004). Inter-residue Interactions in Protein Folding and Stability. Prog. Biophys. Mol. Biol. 86, 235-277. REVIEW
 
M. Michael Gromiha, J.G. Siebers, S. Selvaraj, H. Kono and A. Sarai (2004). Intermolecular and Intramolecular Readout Mechanisms in Protein-DNA Recognition. J. Mol. Biol. 337, 285-294.
 
A. Bava, M. Michael Gromiha , H. Uedaira, K. Kitajima and A. Sarai (2004). ProTherm, version 4.0: Thermodynamic Database for Proteins and Mutants. Nucl. Acids Res. 32, D120-121.
 
M. Michael Gromiha , S. Ahmad and M. Suwa (2004). Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J. Comp. Chem. 25, 762-767.
 
A. Sarai, S. Selvaraj, M. Michael Gromiha, and H. Kono (2004). Structure-Specificity Relationship in DNA Sequence Recognition by Transcription Factors. Aust. Comput. Sci. Comm. 26, 233-238.
 
M. Michael Gromiha and S. Selvaraj (2004). Folding Mechanism of All-beta Globular Proteins. Prep. Biochem. Biotech. 34, 13-23.
 
S. Ahmad, M. Michael Gromiha and A. Sarai (2004). Analysis and Prediction of DNA-binding Proteins and their Binding Residues based on Composition, Sequence and Structural Information. Bioinformatics 20, 477-486.
 
M. Michael Gromiha, C. Santhosh and M. Suwa (2004). Influence of Cation-pi Interactions in Protein-DNA Complexes. Polymer 45, 633-639.
 
S. Ahmad, M. Michael Gromiha, H. Fawareh and A. Sarai (2004). ASAView: Database and tool for solvent accessibility representation in proteins. BMC Bioinformatics 5, 51.
 
M. Michael Gromiha, K. Saraboji, S. Ahmad, M.N. Ponnuswamy and M. Suwa (2004). Role of non-covalent interactions for determining the folding rate of two-state proteins. Biophys. Chem. 107, 263-272.
 
H. Uedaira, M. Michael Gromiha and A. Sarai (2004). Thermodynamic Databases for Biomolecules: Proteins and Mutants. In "Comprehensive Handbook of Calorimetry and Thermal Analysis" (Ed. The Japanese Society of Calorimetry and Thermal Analysis), John Wiley & Sons Ltd. pp 276-279.
 
M. Michael Gromiha and D.A.D. Parry (2004). Characteristic Features of Amino Acid Residues in Coiled-coil Protein Structures. Biophysical Chem. 111, 95-103.
 
S. Selvaraj and M. Michael Gromiha (2004). Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins. PROTEINS: Struct. Funct. Bioinf. 55, 1023-1035
.
M. Michael Gromiha, C. Santhosh and S. Ahmad (2004). Structural Analysis of Cation-pi Interactions in DNA Binding Proteins. Int. J. Biol. Macromol. 34, 203-211.
 
J.Y. Wang, S. Ahmad M. Michael Gromiha, and A. Sarai (2004). Look-up Tables for Protein Solvent Accessibility Prediction and Nearest Neighbor Effect Analysis. Biopolymers 75, 209-216.
 
M. Michael Gromiha, G. Pujadas, C. Magyar, S. Selvaraj and I. Simon (2004). Locating the Stabilizing Residues in (alpha/beta)8 Barrel Proteins Based on Hydrophobicity, Long-Range Interactions, and Sequence Conservation. PROTEINS: Struct. Funct. Bioinformatics 55, 316-329.
 

2003

M. Michael Gromiha (2003). Influence of Inter-residue Interactions in Protein Structures. J. Biophys. Soc. Jpn 43, 87-92. (INVITED REVIEW)
 
S. Ahmad, M. Michael Gromiha and A. Sarai (2003). Real Value Prediction of Solvent Accessibility from Amino Acid Sequence. PROTEINS: Struct. Funct. Genet. 50, 629-635.
 
M. Michael Gromiha (2003). Influence of Cation-pi Interactions in Different Folding Types of Membrane Proteins. Biophys. Chem. 103, 251-258.
 
S. Selvaraj and M. Michael Gromiha (2003). Role of Hydrophobic Clusters and Long-range Contact Networks in the Folding of (alpha/beta)8 Barrel Proteins. Biophysical Journal 84, 1919-1925.
 
M. Michael Gromiha (2003). Factors Influencing the Thermal Stability of Buried Protein Mutants. Polymer 44, 4061-4066.
 
S. Ahmad, M. Michael Gromiha and A. Sarai (2003). RVP-Net: Online Prediction of Real Valued Accessible Surface Area of Proteins from Single Sequences. Bioinformatics 19, 1849-1851.
 
M. Michael Gromiha and Makiko Suwa (2003). Variation of Amino Acid Properties in All-beta Globular and Outer Membrane Protein Structures. Int. J. Biol. Macromol. 32, 93-98.
 
S. Ahmad and M. Michael Gromiha (2003). Design and Training of a Neural Network for Predicting the Solvent Accessibility of Proteins. J. Comp. Chem. 24, 1313-1320.
 
M. Michael Gromiha (2003). Importance of Native-state Topology for Determining the Folding Rate of Two-state Proteins. J. Chem. Inf. Comp. Sci. 43, 1481-1485.

2002

Recent Research Developments in Protein Folding, Stability and Design (2002). M. Michael Gromiha and S. Selvaraj (Editors), Research Signpost, Trivandrum, India.
 
M. Michael Gromiha and S. Selvaraj (2002). Important Amino Acid Properties for Determining the Transition State Structures of Two-state Protein Mutants. FEBS Letters 526, 129-134.
 
A. Sarai, M. Michael Gromiha, J. An, P. Prabakaran, S. Selvaraj, H. Kono, M. Oobatake and H. Uedaira (2002). Thermodynamic Databases for Proteins and Protein-Nucleic Acid Interactions. Biopolymers 61, 121-126.
 
S. Selvaraj and M. Michael Gromiha (2002). Role of Inter-Residue Interactions in the Folding of (alpha/beta)8 Barrel Proteins. Recent Res. Devel. Protein Fold. Stab. Des. (Eds. M. Michael Gromiha and S. Selvaraj), Research Sign Post, Trivandrum, India pp 57-66.
 
M. Michael Gromiha, M. Oobatake, H. Kono, H. Uedaira and A. Sarai (2002). Importance of Mutant Position in Ramachandran Plot for Predicting Protein Stability of Surface Mutations. Biopolymers 64, 210-220.
 
H. Uedaira, M. Michael Gromiha, K. Kitajima and A. Sarai (2002). ProTherm: Thermodynamic Database for Proteins and Mutants. J. Biophys. Soc. Jpn 42, 276-278. (REVIEW)
 
S. Ahmad and M. Michael Gromiha (2002). NETASA: Neural Network Based Prediction of Solvent Accessibility. Bioinformatics 18, 819-824.
 
M. Michael Gromiha (2002). Influence of Cation-pi Interactions in Mesophilic and Thermophilic Proteins. J. Liquid Chromat. Rel. Tech. 25, 3139-3147.
 
T. Yoshida, T. Nishimura, M. Aida, F. Pichierri, M. Michael Gromiha and A. Sarai (2002). Evaluation of Free Energy Landscape for Base-Amino Acid Interactions using Ab initio Force Field and Extensive Sampling. Biopolymers 61, 84-95.
 
M. Michael Gromiha, H. Uedaira, J. An, S. Selvaraj, P. Prabakaran and A. Sarai (2002). ProTherm, Thermodynamic Database for Proteins and Mutants: Developments in Version 3.0. Nucl. Acids Res. 30, 301-302.
 
T.S. Kumarevel, M. Michael Gromiha, S. Selvaraj, K. Gayatri and P.K.R. Kumar (2002). Influence of Medium and Long-range Interactions in Different Folding types of Globular Proteins. Biophys. Chem. 99, 189-198.
 
M. Michael Gromiha, S. Thomas and C. Santhosh (2002). Role of cation-pi interactions to the stability of thermophilic proteins. Prep. Biochem. Biotech. 32, 355-362.
 
A. Sarai, P. Prabakaran, M. Michael Gromiha, K. Kitajima and H. Uedaira (2002). ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions. J. Biophys. Soc. Jpn 42, 279-281. (REVIEW)
 

2001

M. Michael Gromiha and S. Selvaraj (2001). Comparison between Long-range Interactions and Contact Order in Determining the Folding Rate of Two-state Proteins: Application of Long Range Order to Folding Rate Prediction. J. Mol. Biol. 310, 27-32.
 
M. Michael Gromiha (2001). Factors Influencing the Stability of Alpha Helices and Beta Strands in Thermophilic Ribonuclease H. Prep. Biochem. Biotech. 31, 103-112.
 
N. Kannan, S.Selvaraj, M. Michael Gromiha and S.Vishveshwara (2001). Residue Clusters in (alpha/beta)8 Barrel proteins:Implications for Structure, Function and folding. Proteins: Struct. Funct. Genetics 43, 103-112.
 
M. Michael Gromiha (2001). ProTherm: Thermodynamic Database for Proteins and Mutants. Nucl. Acids Res. online (http://www3.oup.co.uk/nar/)
 
T.S. Kumarevel, M. Michael Gromiha and M.N. Ponnuswamy (2001). Distribution of Amino Acid Residues and Residue-Residue Contacts in Molecular Chaperones. Prep. Biochem. Biotech. 31, 163-183.
 
M. Michael Gromiha and S. Selvaraj (2001). Role of Medium and Long-range Interactions in Discriminating Globular and Membrane Proteins. Int. J. Biol. Macromol. 29, 25-34.
 
P. Prabakaran, J. An, M. Michael Gromiha , S. Selvaraj, H. Uedaira, H. Kono and A. Sarai (2001). Thermodynamic Database for Protein-Nucleic Acid Interactions (ProNIT). Bioinformatics 17, 1027-1034.
 
M. Michael Gromiha (2001). Prediction of Secondary Structures in Globular and Membrane Proteins. Recent Research Devel. Protein Eng. 2, 161-178 (INVITED REVIEW).
 
P. Kaliannan, M. Michael Gromiha and M. Elanthirayan (2001). Solvent Accessibility Studies on Polysaccarides. Int. J. Biol. Macromol. 28, 135-141.
 
M. Michael Gromiha (2001). Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins. Biophys. Chem. 91, 71-77.
 
M. Michael Gromiha and A. Mary Thangakani (2001). Role of Medium and Long-range Interactions to the Stability of the Mutants of T4 Lysozyme. Prep. Biochem. Biotech. 31, 217-227.
 

2000

M. Michael Gromiha , J. An, H. Kono, M. Oobatake, H. Uedaira, P. Prabakaran and A. Sarai (2000). ProTherm, Version 2.0: Thermodynamic Database for Proteins and Mutants. Nucl. Acids Res. 28, 283-285.
 
S. Selvaraj and M. Michael Gromiha (2000). Inter-residue Interactions in Protein Structures. Current Science 78, 129-131.
 
M. Michael Gromiha (2000). Structure Based Sequence Dependent Stiffness Scale for Trinucleotides: A Direct Method. J. Biol. Phys. 26, 41-48.
 
K. Sayano, H. Kono, M. Michael Gromiha and A. Sarai (2000). Multicanonical Monte Carlo Calculation of the Free Energy Map of the Base-Amino Acid Interaction. J. Comp. Chem. 21, 954-962.
 
M. Michael Gromiha, J. An, H. Kono, M. Oobatake, H. Uedaira, P. Prabakaran, S. Selvaraj and A. Sarai (2000). Recent Developments of ProTherm: Thermodynamic Database for Proteins and Mutants. Genome Informatics 11, 384-385.
 
R. Muthusamy, M. Michael Gromiha and P.K. Ponnuswamy (2000). On the Thermal Unfolding Character of Globular Proteins. J. Prot. Chem. 19, 1-8.
 
M. Michael Gromiha and S. Selvaraj (2000). Inter-residue Interactions in the Structure, Folding and Stability of Proteins. Recent Research Devel. Biophys. Chem. 1, 1-14 (INVITED REVIEW) .
 
T.S. Kumarevel, M. Michael Gromiha and M.N. Ponnuswamy (2000). Structural Class Prediction: An Application of Residue Distribution Along the Sequence. Biophys. Chem. 88, 81-101.
 
H. Uedaira, M. Michael Gromiha, J. An and A. Sarai (2000). Introduction to the Thermodynamic Database for Proteins and Mutants, ProTherm. Netsu Sokutei (Calorimetry and Thermal Analysis) 27, 250-256.
 
M. Michael Gromiha , M. Oobatake, H. Kono, H. Uedaira and A. Sarai (2000). Importance of Surrounding Residues for Predicting Protein Stability of Partially Buried Mutations. J. Biomol. Str. Dyn. 18, 281-295.
 
P. Prabakaran, J. An, M. Michael Gromiha, S. Selvaraj, H. Uedaira, H. Kono and A. Sarai (2000). ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions. Genome Informatics 11, 386-387

1999

M. Michael Gromiha , J. An, H. Kono, M. Oobatake, H. Uedaira and A. Sarai (1999). ProTherm: Thermodynamic Database for Proteins and Mutants. Nucl. Acids Res. 27, 286-288.
 
M. Michael Gromiha and S. Selvaraj (1999). Influence of Medium and Long Range Contacts in Protein Folding. Prep. Biochem. Biotech. 29, 339-351.
 
M. Michael Gromiha and S. Selvaraj (1999). Importance of Long Range Interactions in Protein Folding. Biophysical Chemistry 77, 49-68.
 
K. Sayano, H. Kono, M. Michael Gromiha, and A. Sarai (1999). Application of Multicanonical Algorithm for the derivation of Free-energy Landscape of Base-amino acid Interactions. RIKEN REVIEW 25, 141-142.
 
P. Prabakaran, J. An, M. Michael Gromiha, S. Selvaraj, H. Uedaira, H. Kono and A. Sarai (1999). Thermodynamic Database for Protein-DNA Interactions. Genome Informatics 10, 280-281.
 
M. Michael Gromiha (1999). A Simple Method for Predicting Transmembrane Alpha Helices at Better Accuracy. Protein Engineering 12, 557-561.
 
M. Michael Gromiha , M. Oobatake, H. Kono, H. Uedaira and A. Sarai (1999). Role of Structural and Sequence Information for Predicting Protein Stability Changes: Comparison between Buried and Partially Buried Mutations. Protein Engineering 12, 549-555.
 
A. Sarai, H. Kono, M. Michael Gromiha, F. Pichierri, K. Sayano and M. Aida (1999). Methods for Predicting Target Sites of Transcription Factors. Genome Informatics 10, 247-248.
 
M. Michael Gromiha , M. Oobatake, H. Kono, H. Uedaira and A. Sarai (1999). Relationship between Amino Acid Properties and Protein Stability: Buried Mutations. J. Protein Chem. 18, 565- 578.
 
F. Pichierri, M. Aida, M. Michael Gromiha and A. Sarai (1999). Free Energy Maps of Base-Amino Acid Interactions for Protein-DNA Recognition. J. Amer. Chem. Soc. 121, 6152-6157
 
M. Michael Gromiha, H. Kono, K. Sayano, F. Pichierri, M. Aida and A. Sarai (1999). Free Energy Maps of Interaction between Base pairs and Amino acids: Effect of Side-chain Length. RIKEN REVIEW 25, 134-135.
 
M. Michael Gromiha, M. Oobatake and A. Sarai (1999). Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophysical Chemistry 82, 51-67.
 
M. Michael Gromiha and S. Selvaraj (1999). Amino Acid Clustering Pattern and Medium and Long-range Interactions in (alpha/beta)8 Barrel Proteins. Periodicum Biologorum 101, 333-338.
 
M. Michael Gromiha , J. An, H. Kono, M. Oobatake, H. Uedaira, P. Prabakaran and A. Sarai (1999) Progress of ProTherm: Thermodynamic Database for Proteins and Mutants. Genome Informatics 10, 265-266.

1998

T.S. Kumarevel, M. Michael Gromiha , and M.N. Ponnuswamy (1998). Solvent Accessibility Analysis on the Mutants of Hsc70 ATPase fragment. Biophysical Chemistry 71 99-111
 
M.G. Munteanu, M. Michael Gromiha and S. Pongor (1998). Non-linear Behaviour of Anisotropic Elastic Bending Models of DNA. Nonlinear Science Today S09389008(98)00002-3; NST URL (http://www.springer-ny.com/nst)
 
M. Michael Gromiha and S. Selvaraj (1998). Protein Secondary Structure Prediction in Different Structural Classes. Protein Engineering 11 249-251
 
S. Selvaraj and M. Michael Gromiha (1998). Analysis of Amino Acid Clustering Pattern in TIM barrel Proteins. J. Protein Chem. 17 407-415
 
A. Gabrielian, K. Vlahovicek, M.G. Munteanu, M. Michael Gromiha , I. Brukner, R. Sanchez and S. Pongor (1998). Prediction of Bendability and Curvature in Genomic DNA. In "Biomolecular Structure and Dynamics (Eds. R.H. Sharma and M.H. Sharma) Vol. 1 117-132, Adenine Press, New York.
 
P. Kaliannan, M. Michael Gromiha, K. Ramamurthi and M. Elanthirayan (1998). Solvent Accessibility Analysis on Glycosaminoglycons. Biophysical Chemistry 74, 11-22
 
S. Selvaraj and M. Michael Gromiha (1998). Importance of Long Range Interactions in TIM Barrel Fold. J. Protein Chem. 17, 691-697
 
F. Pichierri, M. Michael Gromiha , M. Aida and A. Sarai (1998). Free-Energy Calculations of Base-Amino Acid Interactions in DNA-Protein Recognition. RIKEN Review 19, 130-131.
 
T.S. Kumarevel, M. Michael Gromiha and M.N. Ponnuswamy (1998). Analysis of Hydrophobic and Charged Patches and Influence of Medium and Long Range Contacts in Molecular Chaperones. Biophysical Chemistry 75, 105-113.
 
M. Michael Gromiha , J. An, H. Kono, M. Oobatake, H. Uedaira and A. Sarai (1998) ProTherm: Thermodynamic Database for Proteins and Mutants. Genome Informatics 9, 330-331.
 
T.S. Kumarevel, M. Michael Gromiha and M.N. Ponnuswamy (1998). Molecular Chaperones. Current Sci. 75, 1000-1002.

1997

M. Michael Gromiha , R. Majumdar and P.K. Ponnuswamy (1997). Identification of Membrane Spanning Beta Strands in Bacterial Porins. Protein Engineering 10 497-500
 
M. Michael Gromiha and S. Selvaraj. (1997). Influence of Medium and Long Range Interactions in Different Structural Classes of Globular Proteins. J. Biol. Phys. 23 151-162
 
M. Michael Gromiha , M.G. Munteanu, I. Simon and S. Pongor (1997). The Role of DNA Bending in Cro Protein-DNA Interactions. Biophysical Chemistry 69 153-160
 
M. Michael Gromiha , and S. Selvaraj (1997). Influence of Medium and Long Range Contacts in TIM barrel proteins. J. Biol. Phys. 23 209-217

1996

M. Michael Gromiha , M.G. Munteanu, A.Gabrielian and S. Pongor (1996). Anisotropic Elastic Bending Models of DNA. J. Biol. Phys. 22 227-243
 
M. Michael Gromiha and P.K. Ponnuswamy (1996). Hydrophobic Distribution and Spatial Arrangement of Amino Acid Residues in Membrane Proteins. Int. J. Peptide Protein Res. 48 452-460

1995

M. Michael Gromiha and P.K. Ponnuswamy (1995). Prediction of Protein Secondary Structures from their Hydrophobic Characteristics. Int. J. Peptide Protein Res. 45 225-240

1994

P.K. Ponnuswamy and M. Michael Gromiha (1994). On the Conformational Stability of Folded Proteins. J. Theor. Biol. 166 63-74.
 
P.K. Ponnuswamy and M. Michael Gromiha (1994). On the Conformational Stability of Oligonucleotide Duplexes and tRNA Molecules. J. Theor. Biol. 169 419-432

1993

P.K. Ponnuswamy and M. Michael Gromiha (1993). Prediction of Transmembrane Helices from Hydrophobic Characteristics of Proteins. Int. J. Peptide Protein Res. 42 326-341.
 
M. Michael Gromiha and P.K. Ponnuswamy (1993). Prediction of Transmembrane Beta Strands from Hydrophobic Characteristics of Proteins. Int. J. Peptide Protein Res. 42 420-431
 
M. Michael Gromiha and P.K. Ponnuswamy (1993). Relationship between Amino Acid Properties and Protein Compressibility. J. Theor. Biol. 165 87-100.