Tom L. Blundell

According to our database, Tom L. Blundell authored at least 57 papers between 1994 and 2024.

Collaborative distances:

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

2024

Structure-based drug design with equivariant diffusion models.

Arne Schneuing, Charles Harris, Yuanqi Du, Kieran Didi, Arian Rokkum Jamasb, Ilia Igashov, Weitao Du, Carla P. Gomes, Tom L. Blundell, Pietro Lio, Max Welling, Michael M. Bronstein, Bruno E. Correia

Nat. Comput. Sci., December, 2024

Machine learning-aided generative molecular design.

Yuanqi Du, Arian R. Jamasb, Jeff Guo, Tianfan Fu, Charles Harris, Yingheng Wang, Chenru Duan, Pietro Liò, Philippe Schwaller, Tom L. Blundell

Nat. Mac. Intell., 2024

Evaluating Representation Learning on the Protein Structure Universe.

Arian Rokkum Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell

Proceedings of the Twelfth International Conference on Learning Representations, 2024

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

Structure-based Drug Design with Equivariant Diffusion Models.

Arne Schneuing, Yuanqi Du, Charles Harris, Arian R. Jamasb, Ilia Igashov, Weitao Du, Tom L. Blundell, Pietro Lió, Carla Gomes, Max Welling, Michael M. Bronstein, Bruno E. Correia

CoRR, 2022

Structural landscapes of PPI interfaces.

Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher

Briefings Bioinform., 2022

Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA.

Martin Bartas, Adriana Volná, Christopher A. Beaudoin, Ebbe Toftgaard Poulsen, Jirí Cerven, Václav Brázda, Vladimír Spunda, Tom L. Blundell, Petr Pecinka

Briefings Bioinform., 2022

Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks.

Arian R. Jamasb, Ramón Viñas Torné, Eric Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lió, Tom L. Blundell

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

2021

Three Simple Properties Explain Protein Stability Change upon Mutation.

Octav Caldararu, Tom L. Blundell, Kasper P. Kepp

J. Chem. Inf. Model., 2021

A base measure of precision for protein stability predictors: structural sensitivity.

Octav Caldararu, Tom L. Blundell, Kasper P. Kepp

BMC Bioinform., 2021

ProtCHOIR: a tool for proteome-scale generation of homo-oligomers.

Pedro H. M. Torres, Artur D. Rossi, Tom L. Blundell

Briefings Bioinform., 2021

Utilizing graph machine learning within drug discovery and development.

Thomas Gaudelet, Ben Day, Arian R. Jamasb, Jyothish Soman, Cristian Regep, Gertrude Liu, Jeremy B. R. Hayter, Richard Vickers, Charles Roberts, Jian Tang, David Roblin, Tom L. Blundell, Michael M. Bronstein, Jake P. Taylor-King

Briefings Bioinform., 2021

COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets.

Ali F. Alsulami, Pedro H. M. Torres, Ismail Moghul, Sheikh Mohammed Arif, Amanda K. Chaplin, Sundeep Chaitanya Vedithi, Tom L. Blundell

Briefings Bioinform., 2021

SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets.

Ali F. Alsulami, Sherine E. Thomas, Arian R. Jamasb, Christopher A. Beaudoin, Ismail Moghul, Bridget Bannerman, Liviu Copoiu, Sundeep Chaitanya Vedithi, Pedro Torres, Tom L. Blundell

Briefings Bioinform., 2021

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

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.

Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Robert D. Finn, Julian Gough, David T. Jones, Lawrence A. Kelley, Typhaine Paysan-Lafosse, Su Datt Lam, Alexey G. Murzin, Arun Prasad Pandurangan, Gustavo A. Salazar, Marcin J. Skwark, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo

Nucleic Acids Res., 2020

ProCarbDB: a database of carbohydrate-binding proteins.

Liviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra

Nucleic Acids Res., 2020

Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design.

Peter R. Curran, Chris J. Radoux, Mihaela D. Smilova, Richard A. Sykes, Alicia P. Higueruelo, Anthony R. Bradley, Brian D. Marsden, David R. Spring, Tom L. Blundell, Andrew R. Leach, William R. Pitt, Jason C. Cole

J. Chem. Inf. Model., 2020

Systematic Investigation of the Data Set Dependency of Protein Stability Predictors.

Octav Caldararu, Rukmankesh Mehra, Tom L. Blundell, Kasper P. Kepp

J. Chem. Inf. Model., 2020

Utilising Graph Machine Learning within Drug Discovery and Development.

Thomas Gaudelet, Ben Day, Arian R. Jamasb, Jyothish Soman, Cristian Regep, Gertrude Liu, Jeremy B. R. Hayter, Richard Vickers, Charles Roberts, Jian Tang, David Roblin, Tom L. Blundell, Michael M. Bronstein, Jake P. Taylor-King

CoRR, 2020

2019

Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus.

Marcin J. Skwark, Pedro Henrique Monteiro Torres, Liviu Copoiu, Bridget Bannerman-Chukualim, R. Andres Floto, Tom L. Blundell

Database J. Biol. Databases Curation, 2019

2017

SDM: a server for predicting effects of mutations on protein stability.

Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell

Nucleic Acids Res., 2017

XSuLT: a web server for structural annotation and representation of sequence-structure alignments.

Bernardo Ochoa-Montaño, Tom L. Blundell

Nucleic Acids Res., 2017

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species.

Sony Malhotra, Grace Mugumbate, Tom L. Blundell, Alicia P. Higueruelo

Database J. Biol. Databases Curation, 2017

2015

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.

Douglas E. V. Pires, Tom L. Blundell, David B. Ascher

Nucleic Acids Res., 2015

Genome3D: exploiting structure to help users understand their sequences.

Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo

Nucleic Acids Res., 2015

CHOPIN: a web resource for the structural and functional proteome of <i>Mycobacterium tuberculosis</i>.

Bernardo Ochoa-Montaño, Nishita Mohan, Tom L. Blundell

Database J. Biol. Databases Curation, 2015

SInCRe - structural interactome computational resource for <i>Mycobacterium tuberculosis</i>.

Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan

Database J. Biol. Databases Curation, 2015

2014

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.

Douglas E. V. Pires, David B. Ascher, Tom L. Blundell

Nucleic Acids Res., 2014

Does a More Precise Chemical Description of Protein-Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

Pedro J. Ballester, Adrian Schreyer, Tom L. Blundell

J. Chem. Inf. Model., 2014

Polyphony: superposition independent methods for ensemble-based drug discovery.

William R. Pitt, Rinaldo W. Montalvão, Tom L. Blundell

BMC Bioinform., 2014

mCSM: predicting the effects of mutations in proteins using graph-based signatures.

Douglas E. V. Pires, David B. Ascher, Tom L. Blundell

Bioinform., 2014

2013

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Alison L. Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex L. Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, Christine A. Orengo

Nucleic Acids Res., 2013

CREDO: a structural interactomics database for drug discovery.

Adrian Schreyer, Tom L. Blundell

Database J. Biol. Databases Curation, 2013

TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions.

Alicia P. Higueruelo, Harry Jubb, Tom L. Blundell

Database J. Biol. Databases Curation, 2013

2012

USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints.

Adrian Schreyer, Tom L. Blundell

J. Cheminformatics, 2012

2011

SDM - a server for predicting effects of mutations on protein stability and malfunction.

Catherine L. Worth, Robert Preissner, Tom L. Blundell

Nucleic Acids Res., 2011

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database.

George R. Bickerton, Alicia P. Higueruelo, Tom L. Blundell

BMC Bioinform., 2011

2009

Ulla: a program for calculating environment-specific amino acid substitution tables.

Semin Lee, Tom L. Blundell

Bioinform., 2009

BIPA: a database for protein-nucleic acid interaction in 3D structures.

Semin Lee, Tom L. Blundell

Bioinform., 2009

2008

Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures.

Sungsam Gong, Tom L. Blundell

PLoS Comput. Biol., 2008

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms.

Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell

PLoS Comput. Biol., 2008

Structural assembly of two-domain proteins by rigid-body docking.

Tammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio

BMC Bioinform., 2008

2007

A Structural Bioinformatics Approach to the Analysis of nonsynonymous Single nucleotide polymorphisms (nsSNPS) and their Relation to Disease.

Catherine L. Worth, G. Richard J. Bickerton, Adrian Schreyer, Julia R. Forman, Tammy M. K. Cheng, Semin Lee, Sungsam Gong, David F. Burke, Tom L. Blundell

J. Bioinform. Comput. Biol., 2007

Genome bioinformatic analysis of nonsynonymous SNPs.

David F. Burke, Catherine L. Worth, Eva-Maria Priego, Tammy M. K. Cheng, Luc J. Smink, John A. Todd, Tom L. Blundell

BMC Bioinform., 2007

Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities.

Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvão, Tom L. Blundell

Bioinform., 2007

2005

PROVAT - a versatile tool for Voronoi tessellation analysis of protein structures and complexes.

Swanand P. Gore, David F. Burke, Tom L. Blundell

BMC Bioinform., 2005

CHORAL: a differential geometry approach to the prediction of the cores of protein structures.

Rinaldo W. Montalvão, Richard E. Smith, Simon C. Lovell, Tom L. Blundell

Bioinform., 2005

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

Swanand P. Gore, David F. Burke, Tom L. Blundell

Bioinform., 2005

2003

DDBASE2.0: updated domain database with improved identification of structural domains.

A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini

Bioinform., 2003

2001

SCORE: predicting the core of protein models.

Charlotte M. Deane, Quentin Kaas, Tom L. Blundell

Bioinform., 2001

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.

Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell

Bioinform., 2001

2000

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies.

Kenji Mizuguchi, Tom L. Blundell

Bioinform., 2000

Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.

David F. Burke, Charlotte M. Deane, Tom L. Blundell

Bioinform., 2000

1998

JOY: protein sequence-structure representation and analysis.

Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington

Bioinform., 1998

1995

The pattern of common supersecondary structure (motifs) in protein database.

Zhirong Sun, Tom L. Blundell

Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995

1994

Structure-based identification and clustering of protein families and superfamilies.

Stephen D. Rufino, Tom L. Blundell

J. Comput. Aided Mol. Des., 1994