EVA: continuous automatic evaluation of protein structure prediction servers. - Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; András Fiser; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Bioinform., 2001)

Tools for comparative protein structure modeling and analysis. - Narayanan Eswar; Bino John; Nebojsa Mirkovic; András Fiser; Valentin A. Ilyin; Ursula Pieper 001; Ashley C. Stuart; Marc A. Martí-Renom; Mallur S. Madhusudhan; Bozidar Yerkovich; Andrej Sali (Nucleic Acids Res., 2003)

EVA: evaluation of protein structure prediction servers. - Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Nucleic Acids Res., 2003)

MODBASE, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Narayanan Eswar; Hannes Braberg; Mallur S. Madhusudhan; Fred P. Davis; Ashley C. Stuart; Nebojsa Mirkovic; Andrea Rossi 005; Marc A. Martí-Renom; András Fiser; Ben M. Webb; Daniel M. Greenblatt; et al. (Nucleic Acids Res., 2004)

MODBASE: a database of annotated comparative protein structure models and associated resources. - Ursula Pieper 001; Narayanan Eswar; Fred P. Davis; Hannes Braberg; Mallur S. Madhusudhan; Andrea Rossi 005; Marc A. Martí-Renom; Rachel Karchin; Ben M. Webb; David Eramian; Min-Yi Shen; Libusha Kelly; et al. (Nucleic Acids Res., 2006)

DBAli tools: mining the protein structure space. - Marc A. Martí-Renom; Ursula Pieper 001; Mallur S. Madhusudhan; Andrea Rossi 005; Narayanan Eswar; Fred P. Davis; Fátima Al-Shahrour; Joaquín Dopazo; Andrej Sali (Nucleic Acids Res., 2007)

Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability. - Kanika Bajaj; Mallur S. Madhusudhan; Bharat V. Adkar; Purbani Chakrabarti; C. Ramakrishnan; Andrej Sali; Raghavan Varadarajan (PLoS Comput. Biol., 2007)

Structure-guided fragment-based in silico drug design of dengue protease inhibitors. - Tim Knehans; Andreas Schüller; Danny N. Doan; Kassoum Nacro; Jeffrey Hill; Peter Güntert; M. S. Madhusudhan 001; Tanja Weil; Subhash G. Vasudevan (J. Comput. Aided Mol. Des., 2011)

CLICK - topology-independent comparison of biomolecular 3D structures. - M. N. Nguyen; Kuan Pern Tan; Mallur S. Madhusudhan (Nucleic Acids Res., 2011)

ModBase, a database of annotated comparative protein structure models, and associated resources. - Ursula Pieper 001; Benjamin M. Webb; David T. Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C. Meng; Eric F. Pettersen; Conrad C. Huang; Ruchira S. Datta; Parthasarathy Sampathkumar; et al. (Nucleic Acids Res., 2011)

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. - Kuan Pern Tan; Raghavan Varadarajan; Mallur S. Madhusudhan (Nucleic Acids Res., 2011)

SALIGN: a web server for alignment of multiple protein sequences and structures. - Hannes Braberg; Benjamin M. Webb; Elina Tjioe; Ursula Pieper 001; Andrej Sali; Mallur S. Madhusudhan (Bioinform., 2012)

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. - Kuan Pern Tan; Thanh Binh Nguyen 007; Siddharth Patel; Raghavan Varadarajan; Mallur S. Madhusudhan (Nucleic Acids Res., 2013)

TSpred: a web server for the rational design of temperature-sensitive mutants. - Kuan Pern Tan; Shruti Khare; Raghavan Varadarajan; Mallur Srivatsan Madhusudhan (Nucleic Acids Res., 2014)

Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain - Implication in Mechanosensing. - Kinya Hotta; Soumya Ranganathan; Ruchuan Liu; Fei Wu 019; Hiroaki Machiyama; Rong Gao; Hiroaki Hirata; Neelesh Soni; Takashi Ohe; Christopher W. V. Hogue; M. S. Madhusudhan 001; Yasuhiro Sawada (PLoS Comput. Biol., 2014)

Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus. - Sanchita Banerjee; Ankit Roy; M. S. Madhusudhan 001; Hridoy R. Bairagya; Amit Roy (Comput. Biol. Chem., 2019)

Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin. - Minh N. Nguyen; Neeladri Sen; Meiyin Lin; Thomas Leonard Joseph; Candida Vaz; Vivek Tanavde; Luke Way; Ted R. Hupp; Chandra S. Verma 001; M. S. Madhusudhan 001 (J. Chem. Inf. Model., 2019)

Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions. - Ankit A. Roy; Abhilesh S. Dhawanjewar; Parichit Sharma; Gulzar Singh; M. S. Madhusudhan 001 (Nucleic Acids Res., 2019)

A knowledge-based scoring function to assess quaternary associations of proteins. - Abhilesh S. Dhawanjewar; Ankit A. Roy; Mallur S. Madhusudhan (Bioinform., 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)