M.S. Madhusudhan

Publications

1. Dhawanjewar AS, Roy AA, Madhusudhan MS. A knowledge-based scoring function to assess quaternary associations of proteins. Bioinformatics. 2020 Jun 1;36(12):3739-3748. doi: 10.1093/bioinformatics/btaa207. PMID: 32246820.

2. Sen N, Kanitkar TR, Roy AA, Soni N, Amritkar K, Supekar S, Nair S, Singh G, Madhusudhan MS. Predicting and designing therapeutics against the Nipah virus. PLoS Negl Trop Dis. 2019 Dec 12;13(12):e0007419. doi: 10.1371/journal.pntd.0007419. PMID: 31830030; PMCID: PMC6907750.

3. PDBe-KB consortium. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 2020 Jan 8;48(D1):D344-D353. doi: 10.1093/nar/gkz853. PMID: 31584092; PMCID: PMC6943075.

4. Banerjee S, Roy A, Madhusudhan MS, Bairagya HR, Roy A. Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. Comput Biol Chem. 2019 Oct;82:65-73. doi: 10.1016/j.compbiolchem.2019.05.013. Epub 2019 May 30. PMID: 31272063. PDBe-KB consortium. PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 2020 Jan 8;48(D1):D344-D353. doi: 10.1093/nar/gkz853. PMID: 31584092; PMCID: PMC6943075.

5. Mishra KK, Singh SK, Kumar S, Singh G, Sarkar B, Madhusudhan MS, Das A. Water-Mediated Selenium Hydrogen-Bonding in Proteins: PDB Analysis and Gas-Phase Spectroscopy of Model Complexes. J Phys Chem A. 2019 Jul 18;123(28):5995-6002. doi: 10.1021/acs.jpca.9b04159. Epub 2019 Jul 3. PubMed PMID: 31268326.

6. Roy AA, Dhawanjewar AS, Sharma P, Singh G, Madhusudhan MS. Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions. Nucleic Acids Res. 2019 Jul 2;47(W1):W331-W337. doi: 10.1093/nar/gkz368. PubMed PMID: 31114890; PubMed Central PMCID: PMC6602501.

7. Banerjee S, Roy A, Madhusudhan MS, Bairagya HR, Roy A. Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. Comput Biol Chem. 2019 May 30;82:65-73. doi: 10.1016/j.compbiolchem.2019.05.013. [Epub ahead of print] PubMed PMID: 31272063.

8. Nguyen MN, Sen N, Lin M, Joseph TL, Vaz C, Tanavde V, Way L, Hupp T, Verma CS, Madhusudhan MS. Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin. J Chem Inf Model. 2019 Apr 22;59(4):1529-1546. doi: 10.1021/acs.jcim.8b00762. Epub 2019 Mar 8. PubMed PMID: 30794402.

9. Venkatesan N, Wong JF, Tan KP, Chung HH, Yau YH, Cukuroglu E, Allahverdi A, Nordenskiöld L, Göke J, Geifman-Shochat S, Lin VCL, Madhusudhan MS, Su IH. EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms. Oncogene. 2018 Jan 25;37(4):461-477. doi: 10.1038/onc.2017.309. Epub 2017 Oct 2. PubMed PMID: 28967906.

10. Roy A, Nair S, Sen N, Soni N, Madhusudhan MS. In silico methods for design of biological therapeutics. Methods. 2017 Dec 1;131:33-65. doi: 10.1016/j.ymeth.2017.09.008. Epub 2017 Sep 27. Review. PubMed PMID: 28958951.

11. Soni N, Madhusudhan MS. Computational modeling of protein assemblies. Curr Opin Struct Biol. 2017 Jun;44:179-189. doi: 10.1016/j.sbi.2017.04.006. Epub 2017 May 12. Review. PubMed PMID: 28505542.

12. Nguyen TB, Jayaraman P, Bergseng E, Madhusudhan MS, Kim CY, Sollid LM. Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides. J Biol Chem. 2017 Jun 2;292(22):9218-9228. doi: 10.1074/jbc.M117.785139. Epub 2017 Mar 31. PubMed PMID: 28364043; PubMed Central PMCID: PMC5454103.

13. Farheen N, Sen N, Nair S, Tan KP, Madhusudhan MS. Depth dependent amino acid substitution matrices and their use in predicting deleterious mutations. Prog Biophys Mol Biol. 2017 Sep;128:14-23. doi: 10.1016/j.pbiomolbio.2017.02.004. Epub 2017 Feb 15. PubMed PMID: 28212855.

14. Sahoo MR, Gaikwad S, Khuperkar D, Ashok M, Helen M, Yadav SK, Singh A, Magre I, Deshmukh P, Dhanvijay S, Sahoo PK, Ramtirtha Y, Madhusudhan MS, Gayathri P, Seshadri V, Joseph J. Nup358 binds to AGO proteins through its SUMO-interacting motifs and promotes the association of target mRNA with miRISC. EMBO Rep. 2017 Feb;18(2):241-263. doi: 10.15252/embr.201642386. Epub 2016 Dec 30. PubMed PMID: 28039207; PubMed Central PMCID: PMC5286382.

15. Short JM, Liu Y, Chen S, Soni N, Madhusudhan MS, Shivji MK, Venkitaraman AR. High-resolution structure of the presynaptic RAD51 filament on single-stranded DNA by electron cryo-microscopy. Nucleic Acids Res. 2016 Nov 2;44(19):9017-9030. Epub 2016 Sep 5. PubMed PMID: 27596592; PubMed Central PMCID: PMC5100573.

16. Nguyen MN, Sim AY, Wan Y, Madhusudhan MS, Verma C. Topology independent comparison of RNA 3D structures using the CLICK algorithm. Nucleic Acids Res. 2017 Jan 9;45(1):e5. doi: 10.1093/nar/gkw819. Epub 2016 Sep 14. PubMed PMID: 27634929; PubMed Central PMCID: PMC5741206.

17. 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. doi: 10.1021/acs.biochem.5b01383. Epub 2016 Mar 10. PubMed PMID: 26915388.

18. 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. doi: 10.1073/pnas.1509119112. Epub 2015 Jun 8. PubMed PMID: 26056309; PubMed Central PMCID: PMC4485137.

19. 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. doi: 10.1097/QAD.0000000000000419. PubMed PMID: 25102091; PubMed Central PMCID: PMC4198440.

20. 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

21. 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.

22. 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

23. 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.

24. 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

25. 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

26. 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

27. 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

28. M.N. Nguyen and M.S. Madhusudhan. Biological insights from topology independent comparison of protein 3D structures., Nucleic Acids Res 39 e94, 2011

29. 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

30. 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 multiple protein structures based on sequence and structure features., Protein Engineering Design and selection, 22, 569 - 574, 2009

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. M. A. Marti-Renom, M.S. Madhusudhan and A. Sali Alignment of protein sequences by their profiles, Protein Sci, 13 (4) 1071-87, 2004

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. M.S. Madhusudhan and S. Vishveshwara Computer modeling of human angiogenin - dinucleotide substrate interaction, Proteins, 42 (1) 125-35, 2001

53. 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

54. 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

55. 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

56. 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

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

58. 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

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

60. 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

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