PUBLICATIONS

  1. Chakraborty, A., Srimali, S., Topno, R., Ranshur, A., & Madhusudhan, M. S. (2025). MAGNETIC: a web server to fetch gene network based on motif distribution in promoters. Nucleic Acids Research, gkaf420. https://doi.org/10.1093/nar/gkaf420
  2. Chakraborty, A., Devarajan, A., Kumar, K., CS, R., Madhusudhan, M. S., Ratnaparkhi, G. S., & Kamat, S. S. (2025). Bioinformatics Analysis Identifies Sequence Determinants of Enzymatic Activity for the PHARC-Associated Lipase ABHD12. Biochemistry, 64(8), 1852-1863. https://doi.org/10.1021/acs.biochem.4c00865
  3. Chakraborty, A., Chopde, S., & Madhusudhan, M. S. (2025). Motif distribution in genomes gives insights into gene clustering and co-regulation. Nucleic Acids Research, 53(1), gkae1178. https://doi.org/10.1093/nar/gkae1178
  4. Vaidya, K., Rodrigues, G., Gupta, S., Devarajan, A., Yeolekar, M., Madhusudhan, M. S., & Kamat, S. S. (2025). Identification of sequence determinants for the ABHD14 enzymes. Proteins: Structure, Function, and Bioinformatics, 93(1), 255-266. DOI: 10.1002/prot.26632 https://doi.org/10.1002/prot.26632
  5. Mandal, T., Gnanasegaran, S., Rodrigues, G., Kashipathi, S., Tiwari, A., Dubey, A. K., ... & Ghosh, M. (2024). Targeting LLT1 as a potential immunotherapy option for cancer patients non-responsive to existing checkpoint therapies in multiple solid tumors. BMC cancer, 24(1), 1365. doi.org/10.1186/s12885-024-13074-z
  6. Soni, N., & Madhusudhan, M. S. (2024). COCONUT: An analysis of coiled-coil regions in proteins. bioRxiv, 2024-03. https://doi.org/10.1101/2024.03.25.586698
  7. Shanbhag, K., Mhetre, A. B., Saharan, O., Devarajan, A., Rai, A., Madhusudhan, M. S., ... & Kamat, S. S. (2024). Chemical Proteomics Identifies Protein Ligands for Monoacylglycerol Lipids. bioRxiv, 2024-12. https://doi.org/10.1101/2024.12.22.629584
  8. Ghosh, M., Tiwari, A., Dubey, A. K., Bhattacharjee, S., Manjunath, Y., Kashipathi, S., ... & Rodrigues, G. (2024). First-in-human phase 1 clinical trial of ZM008, a monoclonal IgG1 targeting LLT1, monotherapy and in combination with pembrolizumab in advanced solid tumors. Cancer Research, 84(6_Supplement), 7535-7535. https://doi.org/10.1158/1538-7445.AM2024-7535
  9. Mukundan, S., Deshpande, G., & Madhusudhan, M. S. (2024). High-affinity biomolecular interactions are modulated by low-affinity binders. NPJ Systems Biology and Applications, 10(1), 85. https://doi.org/10.1038/s41540-024-00410-z
  10. Soorya, G., Agrawal, D., Bhat, S., Mandal, T., Kashipathi, S., Madhusudhan, M. S., ... & Chirmule, N. (2023). An explainable machine learning data analytics method using TIGIT-linked genes for identifying biomarker signatures to clinical outcomes. bioRxiv, 2023-12. https://doi.org/10.1101/2023.12.05.570321
  11. Madhusudhan, M. S., Ribas, I. G., Ghosh, M., Tiwari, A., Dubey, A., Bhattacharjee, S., ... & Rodrigues, G. (2023). 227P Biomarkers for novel NK checkpoint inhibitor anti LLT1 antibody, ZM008: Patient transcriptome analysis. Annals of Oncology, 34, S272. https://doi.org/10.1016/j.annonc.2023.09.2950
  12. Sen, N., & Madhusudhan, M. S. (2022). A structural database of chain–chain and domain–domain interfaces of proteins. Protein Science, 31(9), e4406. https://doi.org/10.1002/pro.4406
  13. Ramtirtha, Y., & Madhusudhan, M. S. (2022). 3-D structure based prediction of SUMOylation sites. bioRxiv, 2022-08. https://doi.org/10.1101/2022.08.19.504594
  14. Nair, S., & Madhusudhan, M. S. (2022). JEDII: Juxtaposition Enabled DNA-binding Interface Identifier. bioRxiv, 2022-05. https://doi.org/10.1101/2022.05.19.492702
  15. Ramtirtha, Y., & Madhusudhan, M. S. (2022). Prediction of SUMOylation targets in Drosophila melanogaster. bioRxiv, 2022-08. https://doi.org/10.1101/2022.08.19.504577
  16. SINGH, G., Varadi, M., & MADHUSUDHAN, M. (2022). PDBe-KB: collaboratively defining the biological context of structural data. https://doi.org/10.1093/nar/gkab988
  17. Mishra, K. K., Borish, K., Singh, G., Panwaria, P., Metya, S., Madhusudhan, M. S., & Das, A. (2021). Observation of an Unusually Large IR Red-Shift in an Unconventional S–H··· S Hydrogen-Bond. The Journal of Physical Chemistry Letters, 12(4), 1228-1235. https://doi.org/10.1021/acs.jpclett.0c03183
  18. Sanghavi, P., Kumar, P., Roy, A., Madhusudhan, M. S., & Mallik, R. (2021). On and off controls within dynein–dynactin on native cargoes. Proceedings of the National Academy of Sciences, 118(23), e2103383118. https://doi.org/10.1073/pnas.2103383118
  19. Tan, K. P., Singh, K., Hazra, A., & Madhusudhan, M. S. (2021). Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Current Research in Structural Biology, 3, 1-8. https://doi.org/10.1016/j.crstbi.2020.11.002
  20. Kanitkar, T. R., Sen, N., Nair, S., Soni, N., Amritkar, K., Ramtirtha, Y., & Madhusudhan, M. S. (2021). Methods for molecular modelling of protein complexes. Structural Proteomics: High-Throughput Methods, 53-80. https://doi.org/10.1007/978-1-0716-1406-8_3
  21. Deshmukh, P., Markande, S., Fandade, V., Ramtirtha, Y., Madhusudhan, M. S., & Joseph, J. (2021). The miRISC component AGO2 has multiple binding sites for Nup358 SUMO-interacting motif. Biochemical and Biophysical Research Communications, 556, 45-52. https://doi.org/10.1016/j.bbrc.2021.03.140
  22. Tan, K. P., Kanitkar, T. R., Kwoh, C. K., & Madhusudhan, M. S. (2021). Packpred: Predicting the functional effect of missense mutations. Frontiers in Molecular Biosciences, 8, 646288. https://doi.org/10.3389/fmolb.2021.646288
  23. Tan KP, Singh K, Hazra A, Madhusudhan MS. Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations. Curr Res Struct Biol. 2020 Dec 8;3:1-8. https://doi.org/10.1016/j.crstbi.2020.11.002 PMID: 34382009; PMCID: PMC8261469.
  24. Kanitkar TR, Sen N, Nair S, Soni N, Amritkar K, Ramtirtha Y, Madhusudhan MS. Methods for Molecular Modelling of Protein Complexes. Methods Mol Biol. 2021;2305:53-80. https://doi.org/10.1007/978-1-0716-1406-8_3 PMID: 33950384.
  25. Sinnott M, Malhotra S, Madhusudhan MS, Thalassinos K, Topf M. Combining Information from Crosslinks and Monolinks in the Modeling of Protein Structures. Structure. 2020 Sep 1;28(9):1061-1070.e3. https://doi.org/10.1016/j.str.2020.05.012 Epub 2020 Jun 11. PMID: 32531204.
  26. 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. https://doi.org/10.1093/bioinformatics/btaa207 PMID: 32246820; PMCID: PMC7425177.
  27. PDBe-KB: a community-driven resource for structural and functional annotations. PDBe-KB consortium, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D344–D353, https://doi.org/10.1093/nar/gkz853
  28. 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. https://doi.org/10.1371/journal.pntd.0007419 PMID: 31830030; PMCID: PMC6907750.
  29. 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. https://doi.org/10.1016/j.compbiolchem.2019.05.013 Epub 2019 May 30. PMID: 31272063.
  30. 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. https://pubs.acs.org/doi/10.1021/acs.jpca.9b04159 Epub 2019 Jul 3. PMID: 31268326.
  31. 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. https://doi.org/10.1093/nar/gkz368 PMID: 31114890; PMCID: PMC6602501.
  32. 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. https://pubs.acs.org/doi/10.1021/acs.jcim.8b00762 Epub 2019 Mar 8. PMID: 30794402.
  33. 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. http://dx.doi.org/10.1038/onc.2017.309 Epub 2017 Oct 2. PMID: 28967906.
  34. 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. https://doi.org/10.1016/j.ymeth.2017.09.008 Epub 2017 Sep 27. PMID: 28958951.
  35. 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. https://doi.org/10.1016/j.pbiomolbio.2017.02.004 Epub 2017 Feb 15. PMID: 28212855.
  36. 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. https://doi.org/10.1074/jbc.M117.785139 Epub 2017 Mar 31. PMID: 28364043; PMCID: PMC5454103.
  37. Soni N, Madhusudhan MS. Computational modeling of protein assemblies. Curr Opin Struct Biol. 2017 Jun;44:179-189. https://doi.org/10.1016/j.sbi.2017.04.006 Epub 2017 May 12. PMID: 28505542.
  38. 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. https://doi.org/10.15252/embr.201642386 Epub 2016 Dec 30. PMID: 28039207; PMCID: PMC5286382.
  39. 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. https://doi.org/10.1093/nar/gkw819 Epub 2016 Sep 14. PMID: 27634929; PMCID: PMC5741206.
  40. 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. https://doi.org/10.1093/nar/gkw783 Epub 2016 Sep 5. PMID: 27596592; PMCID: PMC5100573.
  41. 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. https://pubs.acs.org/doi/10.1021/acs.biochem.5b01383 Epub 2016 Mar 10. PMID: 26915388.
  42. 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. https://doi.org/10.1073/pnas.1509119112 Epub 2015 Jun 8. PMID: 26056309; PMCID: PMC4485137.
  43. 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. https://doi.org/10.1097/qad.0000000000000419 PMID: 25102091; PMCID: PMC4198440.
  44. 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. https://doi.org/10.1093/nar/gku319 Epub 2014 Apr 29. PMID: 24782523; PMCID: PMC4086094.
  45. 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. https://doi.org/10.1371/journal.pcbi.1003532 PMID: 24722239; PMCID: PMC3983058.
  46. 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. https://doi.org/10.1093/nar/gkt503 Epub 2013 Jun 12. PMID: 23766289; PMCID: PMC3692129.
  47. 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. https://doi.org/10.1093/protein/gzs049 Epub 2012 Sep 12. PMID: 22972763.
  48. Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS. SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics. 2012 Aug 1;28(15):2072-3. https://doi.org/10.1093/bioinformatics/bts302 Epub 2012 May 21. PMID: 22618536; PMCID: PMC3400954.
  49. Nguyen MN, Madhusudhan MS. Biological insights from topology independent comparison of protein 3D structures. Nucleic Acids Res. 2011 Aug;39(14):e94. https://doi.org/10.1093/nar/gkr348 Epub 2011 May 19. PMID: 21596786; PMCID: PMC3152366.
  50. Nguyen MN, Tan KP, Madhusudhan MS. CLICK--topology-independent comparison of biomolecular 3D structures. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W24-8. https://doi.org/10.1093/nar/gkr393 Epub 2011 May 20. PMID: 21602266; PMCID: PMC3125785.
  51. Tan KP, Varadarajan R, Madhusudhan MS. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W242-8. https://doi.org/10.1093/nar/gkr356 Epub 2011 May 16. PMID: 21576233; PMCID: PMC3125764.
  52. Knehans T, Schüller A, Doan DN, Nacro K, Hill J, Güntert P, Madhusudhan MS, Weil T, Vasudevan SG. Structure-guided fragment-based in silico drug design of dengue protease inhibitors. J Comput Aided Mol Des. 2011 Mar;25(3):263-74. https://doi.org/10.1007/s10822-011-9418-0 Epub 2011 Feb 23. PMID: 21344277.
  53. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan;39(Database issue)465-74. https://doi.org/10.1093/nar/gkq1091 Epub 2010 Nov 19. PMID: 21097780; PMCID: PMC3013688.
  54. Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel. 2009 Sep;22(9):569-74. https://doi.org/10.1093/protein/gzp040 Epub 2009 Jul 8. PMID: 19587024; PMCID: PMC2909824.
  55. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol. 2007 Dec;3(12):e241. https://doi.org/10.1371/journal.pcbi.0030241 PMID: 18069886; PMCID: PMC2134964.
  56. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007 Nov;Chapter 2:Unit 2.9. https://doi.org/10.1002/0471140864.ps0209s50 PMID: 18429317.
  57. Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al- Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. https://doi.org/10.1093/nar/gkm236 Epub 2007 May 3. PMID: 17478513; PMCID: PMC1933139.
  58. Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology. 2007 Mar;148(3):1059-79. https://doi.org/10.1210/en.2006-0683 Epub 2006 Dec 14. PMID: 17170095.
  59. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006 Oct;Chapter 5:Unit-5.6. https://doi.org/10.1002/0471250953.bi0506s15 PMID: 18428767; PMCID: PMC4186674.
  60. Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Protein complex compositions predicted by structural similarity. Nucleic Acids Res. 2006 May 31;34(10):2943-52. https://doi.org/10.1093/nar/gkl353 PMID: 16738133; PMCID: PMC1474056.
  61. Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. Variable gap penalty for protein sequence-structure alignment. Protein Eng Des Sel. 2006 Mar;19(3):129-33. https://doi.org/10.1093/protein/gzj005 Epub 2006 Jan 19. PMID: 16423846.
  62. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006 Jan 1;34(Database issue)291-5. https://doi.org/10.1093/nar/gkj059 PMID: 16381869; PMCID: PMC1347422.
  63. Yasuda S, Morokawa N, Wong GW, Rossi A, Madhusudhan MS, Sali A, Askew YS, Adachi R, Silverman GA, Krilis SA, Stevens RL. Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22. Blood. 2005 May 15;105(10):3893-901. https://doi.org/10.1182/blood-2003-10-3501 Epub 2005 Feb 8. PMID: 15701722; PMCID: PMC1895090.
  64. Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Sci. 2004 Apr;13(4):1071-87. https://doi.org/10.1110/ps.03379804 PMID: 15044736; PMCID: PMC2280052.
  65. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 1;32(Database issue)217-22. https://doi.org/10.1093/nar/gkh095 PMID: 14681398; PMCID: PMC308829.
  66. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti- Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3375-80. https://doi.org/10.1093/nar/gkg543 PMID: 12824331; PMCID: PMC168950.
  67. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003 Jul 1;31(13):3311-5. https://doi.org/10.1093/nar/gkg619 PMID: 12824315; PMCID: PMC169025.
  68. Yang Y, Li L, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL. RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and 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. 2002 Jul 12;277(28):25756-74. https://doi.org/10.1074/jbc.m202575200 Epub 2002 Apr 15. PMID: 11956218.
  69. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002 Mar;10(3):435-40. https://doi.org/10.1016/S0969-2126(02)00731-1 PMID: 12005441.
  70. Wong GW, Yasuda S, Madhusudhan MS, Li L, Yang Y, Krilis SA, Sali A, Stevens RL. 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. 2001 Dec 28;276(52):49169-82. https://doi.org/10.1074/jbc.m108677200 Epub 2001 Oct 15. PMID: 11602603.
  71. Eyrich VA, Martí-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001 Dec;17(12):1242-3. https://doi.org/10.1093/bioinformatics/17.12.1242 PMID: 11751240.
  72. Madhusudhan MS, Sanjeev BS, Vishveshwara S. 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. 2001 Oct 1;45(1):30-9. https://doi.org/10.1002/prot.1120 PMID: 11536357.
  73. Madhusudhan MS, Vishveshwara S. Deducing hydration sites of a protein from molecular dynamics simulations. J Biomol Struct Dyn. 2001 Aug;19(1):105-14. https://doi.org/10.1080/07391102.2001.10506724 PMID: 11565842.
  74. Wong GW, Li L, Madhusudhan MS, Krilis SA, Gurish MF, Rothenberg ME, Sali A, Stevens RL. Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. J Biol Chem. 2001 Jun 8;276(23):20648-58. https://doi.org/10.1074/jbc.m010422200 Epub 2001 Mar 20. PMID: 11259427.
  75. Vishveshwara S, Madhusudhan MS, Maizel JV 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. 2001 Feb 15;89(2-3):105-17. https://doi.org/10.1016/S0301-4622(00)00221-0 PMID: 11254205.
  76. Madhusudhan MS, Vishveshwara S, Das A, Kalra P, Jayaram B. 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. 2001 Feb- Apr;38(1-2):27-33. PMID: 11563327.
  77. Madhusudhan MS, Vishveshwara S. Computer modeling of human angiogenin- dinucleotide substrate interaction. Proteins. 2001 Jan 1;42(1):125-35. https://doi.org/10.1002/1097-0134(20010101)42:1%3C125::AID-PROT120%3E3.0.CO;2-K PMID: 11093266.
  78. Sánchez R, Pieper U, Melo F, Eswar N, Martí-Renom MA, Madhusudhan MS, Mirković N, Sali A. Protein structure modeling for structural genomics. Nat Struct Biol. 2000 Nov;7 Suppl:986-90. https://doi.org/10.1038/80776 PMID: 11104007.
  79. M.S. Madhusudhan and S.Vishveshwara Molecular Dynamics Simulations of Modelled Angiogenin-Mononucleotide Complexes, Current Science, 78 (7) 852-857, 2000 www.jstor.org/stable/24103964
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