M. S. Madhusudhan

According to our database, M. S. Madhusudhan authored at least 21 papers between 2001 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

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, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2022

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, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2020

A knowledge-based scoring function to assess quaternary associations of proteins.

Abhilesh S. Dhawanjewar, Ankit A. Roy, Mallur S. Madhusudhan

Bioinform., 2020

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

Nucleic Acids Res., 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, M. S. Madhusudhan

J. Chem. Inf. Model., 2019

Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus <i>Termitomyces clypeatus</i>.

Sanchita Banerjee, Ankit Roy, M. S. Madhusudhan, Hridoy R. Bairagya, Amit Roy

Comput. Biol. Chem., 2019

2014

Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain - Implication in Mechanosensing.

Kinya Hotta, Soumya Ranganathan, Ruchuan Liu, Fei Wu, Hiroaki Machiyama, Rong Gao, Hiroaki Hirata, Neelesh Soni, Takashi Ohe, Christopher W. V. Hogue, M. S. Madhusudhan, Yasuhiro Sawada

PLoS Comput. Biol., 2014

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

2013

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK_a of ionizable residues in proteins.

Kuan Pern Tan, Thanh Binh Nguyen, Siddharth Patel, Raghavan Varadarajan, Mallur S. Madhusudhan

Nucleic Acids Res., 2013

2012

SALIGN: a web server for alignment of multiple protein sequences and structures.

Hannes Braberg, Benjamin M. Webb, Elina Tjioe, Ursula Pieper, Andrej Sali, Mallur S. Madhusudhan

Bioinform., 2012

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

ModBase, a database of annotated comparative protein structure models, and associated resources.

Ursula Pieper, 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, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali

Nucleic Acids Res., 2011

CLICK - topology-independent comparison of biomolecular 3D structures.

M. N. Nguyen, Kuan Pern Tan, Mallur S. Madhusudhan

Nucleic Acids Res., 2011

Structure-guided fragment-based<i> in silico</i> drug design of dengue protease inhibitors.

Tim Knehans, Andreas Schüller, Danny N. Doan, Kassoum Nacro, Jeffrey Hill, Peter Güntert, M. S. Madhusudhan, Tanja Weil, Subhash G. Vasudevan

J. Comput. Aided Mol. Des., 2011

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

DBAli tools: mining the protein structure space.

Marc A. Martí-Renom, Ursula Pieper, Mallur S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, Andrej Sali

Nucleic Acids Res., 2007

2006

MODBASE: a database of annotated comparative protein structure models and associated resources.

Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur S. Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali

Nucleic Acids Res., 2006

2004

MODBASE, a database of annotated comparative protein structure models, and associated resources.

Ursula Pieper, Narayanan Eswar, Hannes Braberg, Mallur S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Martí-Renom, András Fiser, Ben M. Webb, Daniel M. Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali

Nucleic Acids Res., 2004

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

Tools for comparative protein structure modeling and analysis.

Narayanan Eswar, Bino John, Nebojsa Mirkovic, András Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Mallur S. Madhusudhan, Bozidar Yerkovich, Andrej Sali

Nucleic Acids Res., 2003

2001

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