1.U. Grossniklaus, M.S. Madhusudhan and V. Nanjundiah Nonlinear enzyme kinetics can lead to high metabolic flux control coefficients: implications for the evolution of dominance, J Theor Biol, 182 (3) 299-302, 1996
2. M.S. Madhusudhan and S. Vishveshwara Modeling of angiogenin - 3-NMP complex, J Biomol Struct Dyn, 16 (3) 715-22, 1998
3. M.S. Madhusudhan and S. Vishveshwara Comparison of the dynamics of bovine and human angiogenin: a molecular dynamics study, Biopolymers, 49 (2) 131-44, 1999
4. M.S. Madhusudhan and S.Vishveshwara Molecular Dynamics Simulations of Modelled Angiogenin-Mononucleotide Complexes, Current Science, 78 (7) 852-857, 2000
5. R. Sanchez, U. Pieper, F. Melo, N. Eswar, M. A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic and A. Sali Protein structure modeling for structural genomics, Nat Struct Biol, 7 Suppl 986-90, 2000
6. V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali and B. Rost EVA: continuous automatic evaluation of protein structure prediction servers, Bioinformatics, 17 (12) 1242-3, 2001
7. M.S. Madhusudhan, B. S. Sanjeev and S. Vishveshwara Computer modeling and molecular dynamics simulations of ligand bound complexes of bovine angiogenin: dinucleotide topology at the active site of RNase a family proteins, Proteins, 45 (1) 30-9, 2001
8. M.S. Madhusudhan and S. Vishveshwara Deducing hydration sites of a protein from molecular dynamics simulations, J Biomol Struct Dyn, 19 (1) 105-14, 2001
9. M.S. Madhusudhan and S. Vishveshwara Computer modeling of human angiogenin - dinucleotide substrate interaction, Proteins, 42 (1) 125-35, 2001
10. M.S. Madhusudhan, S. Vishveshwara, A. Das, P. Kalra and B. Jayaram A molecular dynamics study based post facto free energy analysis of the binding of bovine angiogenin with UMP and CMP ligands, Indian J Biochem Biophys, 38 (1-2) 27-33, 2001
11. S. Vishveshwara, M.S. Madhusudhan and J. V. Maizel, Jr. Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study, Biophys Chem, 89 (2-3) 105-17, 2001
12. G. W. Wong, L. Li, M.S. Madhusudhan, S. A. Krilis, M. F. Gurish, M. E. Rothenberg, A. Sali and R. L. Stevens Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases, J Biol Chem, 276 (23) 20648-58, 2001
13. G. W. Wong, S. Yasuda, M.S. Madhusudhan, L. Li, Y. Yang, S. A. Krilis, A. Sali and R. L. Stevens Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells, J Biol Chem, 276 (52) 49169-82, 2001
14. A.Sali, M.A.Martí-Renom, M.S. Madhusudhan, A.Fiser and B.Rost “Reply to Moult et al” in Matters Arising, Structure, 10 292-293, 200215. M. A. Marti-Renom(*), M.S. Madhusudhan(*), A. Fiser, B. Rost and A. Sali Reliability of assessment of protein structure prediction methods, Structure, 10 (3) 435-40, 2002 (*) equal contribution
16. Y. Yang, L. Li, G. W. Wong, S. A. Krilis, M.S. Madhusudhan, A. Sali and R. L. Stevens RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calciumand diacylglycerol-binding motifs. Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function, J Biol Chem, 277 (28) 25756-74, 2002
17. N. Eswar, B. John, N. Mirkovic, A. Fiser, V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich and A. Sali Tools for comparative protein structure modeling and analysis, Nucleic Acids Res, 31 (13) 3375-80, 2003
18. I. Y. Koh, V. A. Eyrich, M. A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali and B. Rost EVA: Evaluation of protein structure prediction servers, Nucleic Acids Res, 31 (13) 3311-5, 2003
19. M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A. Stuart, N. Eswar, P. Pieper, N. Mirkovic, M.-Y. Shen and A. Sali. Comparative protein structure modeling. Current Protocols in Bioinformatics. John Wiley & Sons 5 5.1.1-5.1.32 2003
20. M. A. Marti-Renom, M.S. Madhusudhan and A. Sali Alignment of protein sequences by their profiles, Protein Sci, 13 (4) 1071-87, 2004
21. U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F. P. Davis, A. C. Stuart, N. Mirkovic, A. Rossi, M. A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C. C. Huang, T. E. Ferrin and A. Sali MODBASE, a database of annotated comparative protein structure models, and associated resources, Nucleic Acids Res, 32 (Database issue) D217-22, 2004
22. M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.-Y. Shen and A. Sali. Comparitive protein structure modeling. J. M. Walker. The Proteomics Protocols Handbook. Humana Press Inc. Totowa, NJ 831-860 2005
23. S. Yasuda, N. Morokawa, G. W. Wong, A. Rossi, M.S. Madhusudhan, A. Sali, Y. S. Askew, R. Adachi, G. A. Silverman, S. A. Krilis and R. L. Stevens Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22, Blood, 105 (10) 3893-901, 2005
24. F. P. Davis, H. Braberg, M. Y. Shen, U. Pieper, A. Sali and M.S. Madhusudhan. Protein complex compositions predicted by structural similarity, Nucleic Acids Res, 34 (10) 2943-52, 2006
25. M.S. Madhusudhan, M. A. Marti-Renom, R. Sanchez and A. Sali Variable gap penalty for protein sequence-structure alignment, Protein Eng Des Sel, 19 (3) 129-33, 2006
26. U. Pieper, N. Eswar, F. P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B. M. Webb, D. Eramian, M. Y. Shen, L. Kelly, F. Melo and A. Sali MODBASE: a database of annotated comparative protein structure models and associated resources, Nucleic Acids Res, 34 (Database issue) D291-5, 2006
27. K. Bajaj, M.S. Madhusudhan, P. Chakrabarti, C. Ramakrishnan, A. Sali and R. Varadarajan Stereochemical criteria for prediction of the effects of Proline mutations on protein stability, PLoS Computational Biology 3, e241, 2007
28. M. A. Marti-Renom, U. Pieper, M.S. Madhusudhan, A. Rossi, N. Eswar, F. P. Davis, F. Al- Shahrour, J. Dapazo, A. Sali DBAli tools: mining the protein structure space, Nucleic Acids Res,35, W393-397, 2007
29. N. Eswar, M.A. Marti-Renom, B. Webb, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper and A. Sali. Comparative Protein Structure Modeling with MODELLER. Current protocols in bioinformatics. John Wiley & sons Inc. Chapter 2, Unit 2 9, 2007
30. V. D. Winn, R. Haimov-Kochman, A. Paquet, Y. J. Yang, M.S. Madhusudhan, M. Gormley, V. Feng, S. McDonagh, L. Pereira, A. Sali and S. J. Fisher Gene Expression Profiling of the Human Maternal-Fetal Interface Provides Insights into Human Placental Development, Endocrinology, 148 1313-22, 2007
31. M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. Alignment of multiple protein structures based on sequence and structure features., Protein Engineering Design and selection, 22, 569 - 574, 2009
32. U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z.Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, A. Sali. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 39, 465-474, 2011.
33. T. Knehans, A. Schueller, D.N.P. Doan, N. Kassoum, J. Hill, P. Guntert, M.S. Madhusudhan , T. Weil, and S. Vasudevan. Structure-guided fragment-based in silico drug design of dengue protease inhibitors., J. Comput Aided Mol Des, 25 263-274, 2011
34. M.N. Nguyen and M.S. Madhusudhan. Biological insights from topology independent comparison of protein 3D structures., Nucleic Acids Res 39 e94, 2011
35. M.N. Nguyen, K.P. Tan, and M.S. Madhusudhan. CLICK--topology-independent comparison of biomolecular 3D structures., Nucleic Acids Res 39 W24-8, 2011
36. K.P. Tan, R. Varadarajan, M.S. Madhusudhan. Depth: A Web server to compute depth and predict small-molecule binding cavities in proteins., Nucleic Acids Res 39 W242-8, 2011
37. H. Braberg, B. Webb, E. Tijoe, U. Pieper, A. Sali and M.S. Madhusudhan. SALIGN: A multiple protein sequence/structure alignment web server. Bioinformatics, 28 2072-2073 2012
38. D.N.P. Doan, K-Q Li, S. Vasudevan and M.S. Madhusudhan. Transplantation of a hydrogen bonding network from West Nile virus protease onto Dengue-2 protease improves catalytic efficiency and sheds light on substrate specificity. Protein Eng Des Sel, 25(12):843-50, 2012
39. K.P. Tan, T.B. Nguyen, S. Patel, R. Varadarajan and M.S. Madhusudhan. Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins. Nucleic Acids Res 41, W314-321, 2013.
40. K. Hotta S. Ranganathan, R. Liu, F. Wu, H. Machiyama, R. Gao, H. Hirata, N. Soni, T. Ohe, C. W. V. Hogue, M.S. Madhusudhan, and Y. Sawada. Biophysical properties of intrinsically disordered p130Cas substrate domain — implication in mechanosensing. PLoS Computational Biology 10(4): e1003532, 2014
41. K.P. Tan, S. Khare, R. Varadarajan and M.S. Madhusudhan. TSpred: a web server for the rational design of temperature-sensitive mutants. Nucleic Acids Res 42, W277-284, 2014.
42. U. Neogi, S.D. Rao, I. Bontell, J. Verheyen, V.R. Rao, S.C. Gore, N. Soni, A. Shet, E. Schulter, M.L. Ekstrand, A. Wondwossen, R. Kaiser, M.S. Madhusudhan, V.R. Prasad and A. Sonnerborg. AIDS (in press), 2014