Tom L. Blundell

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 24

Top Topics

Machine Learning

Protein Structure

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Database J. Biol. Databases Curation

J. Chem. Inf. Model.

Publications

Yuanqi Du, Arian R. Jamasb, Jeff Guo, Tianfan Fu, Charles Harris, Yingheng Wang, Chenru Duan, Pietro Liò, Philippe Schwaller, Tom L. Blundell
Machine learning-aided generative molecular design. Nat. Mac. Intell. 6 (6) (2024)
Arian R. Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom L. Blundell
Evaluating representation learning on the protein structure universe. CoRR (2024)
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
Evaluating Representation Learning on the Protein Structure Universe. ICLR (2024)
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
Structure-based Drug Design with Equivariant Diffusion Models. CoRR (2022)
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
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50 (D1) (2022)
Arian R. Jamasb, Ramón Viñas Torné, Eric Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lió, Tom L. Blundell
Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction Networks. NeurIPS (2022)
Martin Bartas, Adriana Volná, Christopher A. Beaudoin, Ebbe Toftgaard Poulsen, Jirí Cerven, Václav Brázda, Vladimír Spunda, Tom L. Blundell, Petr Pecinka
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. Briefings Bioinform. 23 (3) (2022)
Carlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher
Structural landscapes of PPI interfaces. Briefings Bioinform. 23 (4) (2022)
Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
A base measure of precision for protein stability predictors: structural sensitivity. BMC Bioinform. 22 (1) (2021)
Pedro H. M. Torres, Artur D. Rossi, Tom L. Blundell
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. Briefings Bioinform. 22 (6) (2021)
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
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets. Briefings Bioinform. 22 (2) (2021)
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
Utilizing graph machine learning within drug discovery and development. Briefings Bioinform. 22 (6) (2021)
Ali F. Alsulami, Pedro H. M. Torres, Ismail Moghul, Sheikh Mohammed Arif, Amanda K. Chaplin, Sundeep Chaitanya Vedithi, Tom L. Blundell
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. Briefings Bioinform. 22 (6) (2021)
Octav Caldararu, Tom L. Blundell, Kasper P. Kepp
Three Simple Properties Explain Protein Stability Change upon Mutation. J. Chem. Inf. Model. 61 (4) (2021)
Liviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra
ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48 (Database-Issue) (2020)
Octav Caldararu, Rukmankesh Mehra, Tom L. Blundell, Kasper P. Kepp
Systematic Investigation of the Data Set Dependency of Protein Stability Predictors. J. Chem. Inf. Model. 60 (10) (2020)
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
Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug Design. J. Chem. Inf. Model. 60 (4) (2020)
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
Utilising Graph Machine Learning within Drug Discovery and Development. CoRR (2020)
Marcin J. Skwark, Pedro Henrique Monteiro Torres, Liviu Copoiu, Bridget Bannerman-Chukualim, R. Andres Floto, Tom L. Blundell
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. Database J. Biol. Databases Curation 2019 (2019)
Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell
SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Bernardo Ochoa-Montaño, Tom L. Blundell
XSuLT: a web server for structural annotation and representation of sequence-structure alignments. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Sony Malhotra, Grace Mugumbate, Tom L. Blundell, Alicia P. Higueruelo
TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. Database J. Biol. Databases Curation 2017 (2017)
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
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43 (Database-Issue) (2015)
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 (2015)
Bernardo Ochoa-Montaño, Nishita Mohan, Tom L. Blundell
. Database J. Biol. Databases Curation 2015 (2015)
Douglas E. V. Pires, Tom L. Blundell, David B. Ascher
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Res. 43 (Database-Issue) (2015)
Douglas E. V. Pires, David B. Ascher, Tom L. Blundell
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
William R. Pitt, Rinaldo W. Montalvão, Tom L. Blundell
Polyphony: superposition independent methods for ensemble-based drug discovery. BMC Bioinform. 15 (2014)
Pedro J. Ballester, Adrian Schreyer, Tom L. Blundell
Does a More Precise Chemical Description of Protein-Ligand Complexes Lead to More Accurate Prediction of Binding Affinity? J. Chem. Inf. Model. 54 (3) (2014)
Douglas E. V. Pires, David B. Ascher, Tom L. Blundell
mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinform. 30 (3) (2014)
Alicia P. Higueruelo, Harry Jubb, Tom L. Blundell
TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. Database J. Biol. Databases Curation 2013 (2013)
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
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 41 (Database-Issue) (2013)
Adrian Schreyer, Tom L. Blundell
CREDO: a structural interactomics database for drug discovery. Database J. Biol. Databases Curation 2013 (2013)
Adrian Schreyer, Tom L. Blundell
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints. J. Cheminformatics 4 (2012)
George R. Bickerton, Alicia P. Higueruelo, Tom L. Blundell
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. BMC Bioinform. 12 (2011)
Catherine L. Worth, Robert Preissner, Tom L. Blundell
SDM - a server for predicting effects of mutations on protein stability and malfunction. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Semin Lee, Tom L. Blundell
BIPA: a database for protein-nucleic acid interaction in 3D structures. Bioinform. 25 (12) (2009)
Semin Lee, Tom L. Blundell
Ulla: a program for calculating environment-specific amino acid substitution tables. Bioinform. 25 (15) (2009)
Sungsam Gong, Tom L. Blundell
Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional Structures. PLoS Comput. Biol. 4 (10) (2008)
Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell
Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms. PLoS Comput. Biol. 4 (7) (2008)
Tammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio
Structural assembly of two-domain proteins by rigid-body docking. BMC Bioinform. 9 (2008)
Richard E. Smith, Simon C. Lovell, David F. Burke, Rinaldo W. Montalvão, Tom L. Blundell
Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities. Bioinform. 23 (9) (2007)
David F. Burke, Catherine L. Worth, Eva-Maria Priego, Tammy M. K. Cheng, Luc J. Smink, John A. Todd, Tom L. Blundell
Genome bioinformatic analysis of nonsynonymous SNPs. BMC Bioinform. 8 (2007)
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
A Structural Bioinformatics Approach to the Analysis of nonsynonymous Single nucleotide polymorphisms (nsSNPS) and their Relation to Disease. J. Bioinform. Comput. Biol. 5 (6) (2007)
Swanand P. Gore, David F. Burke, Tom L. Blundell
PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes. Bioinform. 21 (15) (2005)
Swanand P. Gore, David F. Burke, Tom L. Blundell
PROVAT - a versatile tool for Voronoi tessellation analysis of protein structures and complexes. BMC Bioinform. 6 (S-3) (2005)
Rinaldo W. Montalvão, Richard E. Smith, Simon C. Lovell, Tom L. Blundell
CHORAL: a differential geometry approach to the prediction of the cores of protein structures. Bioinform. 21 (19) (2005)
A. Vinayagam, Jiye Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini
DDBASE2.0: updated domain database with improved identification of structural domains. Bioinform. 19 (14) (2003)
Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinform. 17 (8) (2001)
Charlotte M. Deane, Quentin Kaas, Tom L. Blundell
SCORE: predicting the core of protein models. Bioinform. 17 (6) (2001)
David F. Burke, Charlotte M. Deane, Tom L. Blundell
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure. Bioinform. 16 (6) (2000)
Kenji Mizuguchi, Tom L. Blundell
Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. Bioinform. 16 (12) (2000)
Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington
JOY: protein sequence-structure representation and analysis. Bioinform. 14 (7) (1998)
Zhirong Sun, Tom L. Blundell
The pattern of common supersecondary structure (motifs) in protein database. HICSS (5) (1995)
Stephen D. Rufino, Tom L. Blundell
Structure-based identification and clustering of protein families and superfamilies. J. Comput. Aided Mol. Des. 8 (1) (1994)