List of publications
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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
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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.
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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
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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
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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
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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
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M.N. Nguyen and M.S. Madhusudhan. Biological insights from topology independent
comparison of protein 3D structures., Nucleic Acids Res 39 e94, 2011
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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
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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.
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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M. A. Marti-Renom, M.S. Madhusudhan and A. Sali Alignment of protein sequences by
their
profiles, Protein Sci, 13 (4) 1071-87, 2004
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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
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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
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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
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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
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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
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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
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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
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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
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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
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M.S. Madhusudhan and S. Vishveshwara Computer modeling of human angiogenin -
dinucleotide substrate interaction, Proteins, 42 (1) 125-35, 2001
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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
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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
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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
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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
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M.S. Madhusudhan and S.Vishveshwara Molecular Dynamics Simulations of Modelled
Angiogenin-Mononucleotide Complexes, Current Science, 78 (7) 852-857, 2000
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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
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M.S. Madhusudhan and S. Vishveshwara Modeling of angiogenin - 3-NMP complex, J
Biomol
Struct Dyn, 16 (3) 715-22, 1998
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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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