Publications and Presentations

44. Manjunath GP, Soni N, Vaddavalli PL, Shewale DJ, Madhusudhan MS, Muniyappa K. Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA. Biochemistry. 2016 Mar 29;55(12):1850-62.

43. Bajaj Pahuja K, Wang J, Blagoveshchenskaya A, Lim L, Madhusudhan MS, Mayinger P, Schekman R. Phosphoregulatory protein 14-3-3 facilitates SAC1 transport from the endoplasmic reticulum. Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3199-206.

42. Neogi U, Rao SD, Bontell I, Verheyen J, Rao VR, Gore SC, Soni N, Shet A, Schülter E, Ekstrand ML, Wondwossen A, Kaiser R, Madhusudhan MS, Prasad VR, Sonnerborg A. Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients. AIDS. 2014 Sep 24;28(15):2319-22.

41. Tan KP, Khare S, Varadarajan R, Madhusudhan MS. TSpred: a web server for the rational design of temperature-sensitive mutants. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W277-84.

40. Hotta K, Ranganathan S, Liu R, Wu F, Machiyama H, Gao R, Hirata H, Soni N, Ohe T, Hogue CW, Madhusudhan MS, Sawada Y. Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing. PLoS Comput Biol. 2014 Apr 10;10(4):e1003532.

39. Tan KP, Nguyen TB, Patel S, Varadarajan R, Madhusudhan MS. 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. 2013 Jul;41(Web Server issue):W314-21

38. Doan DN, Li KQ, Basavannacharya C, Vasudevan SG, Madhusudhan MS. 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. 2012 Dec;25(12):843-50.

37. H. Braberg, B. Webb, E. Tijoe, U. Pieper, A. Sali and M.S. Madhusudhan. SALIGN: A multiple protein sequence/structure alignment web server.,in press, Bioinformatics. 2012 Aug 1;28(15):2072-3.

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, 201135.

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

34. M.N. Nguyen and M.S. Madhusudhan. Biological insights from topology independent comparison of protein 3D structures., Nucleic Acids Res 39 e94, 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

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.

31. M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. Alignment of multipleprotein structures based on sequence and structure features., Protein Engineering Design and selection, 22, 569 - 574, 2009

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 theHuman Maternal-Fetal Interface Provides Insights into Human Placental Development, Endocrinolog, 148 1313-22, 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

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

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

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

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

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,

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

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

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

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

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

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

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

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

15. 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

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, 2002

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

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

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

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

9. M. S. Madhusudhan and S. Vishveshwara Computer modeling of human angiogenindinucleotide
substrate interaction, Proteins, 42 (1) 125-35, 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

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,

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

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

4. M.S.Madhusudhan and S.Vishveshwara Molecular Dynamics Simulations of Modelled
Angiogenin-Mononucleotide Complexes, Current Science, 78 (7) 852-857, 2000

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

2. M. S. Madhusudhan and S. Vishveshwara Modeling of angiogenin - 3-NMP complex, J
Biomol Struct Dyn, 16 (3) 715-22, 1998

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