Tom L. Blundell

59 papers A* 2Journal 56Unranked 1

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