Tom L. Blundell - researchr alias

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Viewing Publication 1 - 52 from 52

2022

Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNAMartin Bartas, Adriana Volná, Christopher A. Beaudoin, Ebbe Toftgaard Poulsen, Jirí Cerven, Václav Brázda, Vladimír Spunda, Tom L. Blundell, Petr Pecinka. bib, 23(3), 2022. [doi]

Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Biomolecular Structures and Interaction NetworksArian R. Jamasb, Ramón Viñas Torné 0001, Eric Ma, Yuanqi Du, Charles Harris, Kexin Huang, Dominic Hall, Pietro Lió, Tom L. Blundell. nips 2022: [doi]

Structural landscapes of PPI interfacesCarlos H. M. Rodrigues, Douglas E. V. Pires, Tom L. Blundell, David B. Ascher. bib, 23(4), 2022. [doi]

PDBe-KB: collaboratively defining the biological context of structural dataMihaly 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 0001, 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. nar, 50(D1):534-542, 2022. [doi]

2021

COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targetsAli F. Alsulami, Pedro H. M. Torres, Ismail Moghul, Sheikh Mohammed Arif, Amanda K. Chaplin, Sundeep Chaitanya Vedithi, Tom L. Blundell. bib, 22(6), 2021. [doi]

SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targetsAli 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. bib, 22(2):769-780, 2021. [doi]

A base measure of precision for protein stability predictors: structural sensitivityOctav Caldararu, Tom L. Blundell, Kasper P. Kepp. bmcbi, 22(1):88, 2021. [doi]

Three Simple Properties Explain Protein Stability Change upon MutationOctav Caldararu, Tom L. Blundell, Kasper P. Kepp. jcisd, 61(4):1981-1988, 2021. [doi]

Utilizing graph machine learning within drug discovery and developmentThomas 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. bib, 22(6), 2021. [doi]

ProtCHOIR: a tool for proteome-scale generation of homo-oligomersPedro H. M. Torres, Artur D. Rossi, Tom L. Blundell. bib, 22(6), 2021. [doi]

2020

Systematic Investigation of the Data Set Dependency of Protein Stability PredictorsOctav Caldararu, Rukmankesh Mehra, Tom L. Blundell, Kasper P. Kepp. jcisd, 60(10):4772-4784, 2020. [doi]

ProCarbDB: a database of carbohydrate-binding proteinsLiviu Copoiu, Pedro H. M. Torres, David B. Ascher, Tom L. Blundell, Sony Malhotra. nar, 48(Database-Issue), 2020. [doi]

Hotspots API: A Python Package for the Detection of Small Molecule Binding Hotspots and Application to Structure-Based Drug DesignPeter 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. jcisd, 60(4):1911-1916, 2020. [doi]

PDBe-KB: a community-driven resource for structural and functional annotationsMihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath S. 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 0001, Henry J. Martell, Stuart 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 0001, 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. nar, 48(Database-Issue), 2020. [doi]

2019

Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessusMarcin J. Skwark, Pedro Henrique Monteiro Torres, Liviu Copoiu, Bridget Bannerman-Chukualim, R. Andres Floto, Tom L. Blundell. biodb, 2019, 2019. [doi]

2017

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial speciesSony Malhotra, Grace Mugumbate, Tom L. Blundell, Alicia P. Higueruelo. biodb, 2017, 2017. [doi]

XSuLT: a web server for structural annotation and representation of sequence-structure alignmentsBernardo Ochoa-Montaño, Tom L. Blundell. nar, 45(Webserver-Issue), 2017. [doi]

SDM: a server for predicting effects of mutations on protein stabilityArun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B. Ascher, Tom L. Blundell. nar, 45(Webserver-Issue), 2017. [doi]

2015

Mycobacterium tuberculosisRahul 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. biodb, 2015, 2015. [doi]

Mycobacterium tuberculosisBernardo Ochoa-Montaño, Nishita Mohan, Tom L. Blundell. biodb, 2015, 2015. [doi]

Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexesDouglas E. V. Pires, Tom L. Blundell, David B. Ascher. nar, 43(Database-Issue):387-391, 2015. [doi]

2014

2013

TIMBAL v2: update of a database holding small molecules modulating protein-protein interactionsAlicia P. Higueruelo, Harry Jubb, Tom L. Blundell. biodb, 2013, 2013. [doi]

CREDO: a structural interactomics database for drug discoveryAdrian Schreyer, Tom L. Blundell. biodb, 2013, 2013. [doi]

2012

USRCAT: real-time ultrafast shape recognition with pharmacophoric constraintsAdrian Schreyer, Tom L. Blundell. jcheminf, 4:27, 2012. [doi]

2011

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO databaseGeorge R. Bickerton, Alicia P. Higueruelo, Tom L. Blundell. bmcbi, 12:313, 2011. [doi]

SDM - a server for predicting effects of mutations on protein stability and malfunctionCatherine L. Worth, Robert Preissner, Tom L. Blundell. nar, 39(Web-Server-Issue):215-222, 2011. [doi]

2009

BIPA: a database for protein-nucleic acid interaction in 3D structuresSemin Lee, Tom L. Blundell. bioinformatics, 25(12):1559-1560, 2009. [doi]

Ulla: a program for calculating environment-specific amino acid substitution tablesSemin Lee, Tom L. Blundell. bioinformatics, 25(15):1976-1977, 2009. [doi]

2008

Structural assembly of two-domain proteins by rigid-body dockingTammy M. K. Cheng, Tom L. Blundell, Juan Fernández-Recio. bmcbi, 9, 2008. [doi]

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide PolymorphismsTammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Liò, Tom L. Blundell. ploscb, 4(7), 2008. [doi]

Discarding Functional Residues from the Substitution Table Improves Predictions of Active Sites within Three-Dimensional StructuresSungsam Gong, Tom L. Blundell. ploscb, 4(10), 2008. [doi]

2007

2005

PROVAT - a versatile tool for Voronoi tessellation analysis of protein structures and complexesSwanand P. Gore, David F. Burke, Tom L. Blundell. bmcbi, 6(S-3), 2005. [doi]

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexesSwanand P. Gore, David F. Burke, Tom L. Blundell. bioinformatics, 21(15):3316-3317, 2005. [doi]

CHORAL: a differential geometry approach to the prediction of the cores of protein structuresRinaldo W. Montalvão, Richard E. Smith, Simon C. Lovell, Tom L. Blundell. bioinformatics, 21(19):3719-3725, 2005. [doi]

2003

DDBASE2.0: updated domain database with improved identification of structural domainsA. Vinayagam, J. Shi, Ganesan Pugalenthi, B. Meenakshi, Tom L. Blundell, Ramanathan Sowdhamini. bioinformatics, 19(14):1760-1764, 2003.

2001

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein familiesPaul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, J. Shi, Hiroki Shirai, Tom L. Blundell. bioinformatics, 17(8):748-749, 2001.

SCORE: predicting the core of protein modelsCharlotte M. Deane, Quentin Kaas, Tom L. Blundell. bioinformatics, 17(6):541-550, 2001.

2000

Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structureDavid F. Burke, Charlotte M. Deane, Tom L. Blundell. bioinformatics, 16(6):513-519, 2000.

Analysis of conservation and substitutions of secondary structure elements within protein superfamiliesKenji Mizuguchi, Tom L. Blundell. bioinformatics, 16(12):1111-1119, 2000.

1998

JOY: protein sequence-structure representation and analysisKenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington. bioinformatics, 14(7):617-623, 1998.

1995

The pattern of common supersecondary structure (motifs) in protein databaseZhirong Sun, Tom L. Blundell. hicss 1995: 312-318 [doi]

1994

Structure-based identification and clustering of protein families and superfamiliesStephen D. Rufino, Tom L. Blundell. jcamd, 8(1):5-27, 1994.

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