Michael J E Sternberg

Michael J E Sternberg

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Michael J E Sternberg

Publications by authors named "Michael J E Sternberg"

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Computation Resources for Molecular Biology: Special Issue 2019.

J Mol Biol 2019 Jun 30;431(13):2395-2397. Epub 2019 May 30.

Structural Bioinformatics Group, Centre for Integrative systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.05.034DOI Listing
June 2019

Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?

J Mol Biol 2019 May 14;431(11):2197-2212. Epub 2019 Apr 14.

Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544567PMC
May 2019

Identification of disease-associated loci using machine learning for genotype and network data integration.

Bioinformatics 2019 May 9. Epub 2019 May 9.

Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, United Kingdom.

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http://dx.doi.org/10.1093/bioinformatics/btz310DOI Listing
May 2019

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

J Mol Biol 2018 07 31;430(15):2244-2248. Epub 2018 Jan 31.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, Kensington, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/j.jmb.2018.01.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961936PMC
July 2018

Computation Resources for Molecular Biology: Special Issue 2018.

J Mol Biol 2018 07 31;430(15):2181-2183. Epub 2018 May 31.

Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub Investigator. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.05.041DOI Listing
July 2018

PhenoRank: reducing study bias in gene prioritization through simulation.

Bioinformatics 2018 06;34(12):2087-2095

Department of Life Sciences, Center of Bioinformatics and Systems Biology, Imperial College London, London, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5949213PMC
June 2018

Properties of human genes guided by their enrichment in rare and common variants.

Hum Mutat 2018 03 21;39(3):365-370. Epub 2017 Dec 21.

Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1002/humu.23377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838408PMC
March 2018

Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights.

Hum Mutat 2017 03 11;38(3):289-296. Epub 2017 Jan 11.

Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, UK.

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http://dx.doi.org/10.1002/humu.23155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5748329PMC
March 2017

Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints.

Structure 2017 03 9;25(3):546-558. Epub 2017 Feb 9.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/j.str.2017.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343748PMC
March 2017

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets.

Nucleic Acids Res 2017 02;45(4):1649-1656

Bioinformatics Data Science Group, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, London, UK.

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http://dx.doi.org/10.1093/nar/gkw1248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389551PMC
February 2017

Computation Resources for Molecular Biology: Special Issue 2017.

J Mol Biol 2017 02 23;429(3):345-347. Epub 2016 Dec 23.

Structural Bioinformatics Group, Centre for Integrative systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.12.018DOI Listing
February 2017

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

J Mol Biol 2016 Feb 27;428(4):702-708. Epub 2015 Oct 27.

Structural Bioinformatics Group, Imperial College London, London SW7 2AZ, United Kingdom.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836150061
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http://dx.doi.org/10.1016/j.jmb.2015.10.017DOI Listing
February 2016

Computation Resources for Molecular Biology: A Special Issue.

J Mol Biol 2016 Feb 3;428(4):669-670. Epub 2016 Feb 3.

Journal of Molecular Biology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.jmb.2016.02.001DOI Listing
February 2016

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

BMC Bioinformatics 2015 Oct 23;16:335. Epub 2015 Oct 23.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1186/s12859-015-0771-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619270PMC
October 2015

Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types.

Genome Med 2015 Sep 1;7:95. Epub 2015 Sep 1.

Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1186/s13073-015-0212-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557825PMC
September 2015

Incorporating Virtual Reactions into a Logic-based Ligand-based Virtual Screening Method to Discover New Leads.

Mol Inform 2015 Sep 20;34(9):615-625. Epub 2015 Mar 20.

Department of Bioinformatics, Imperial College London, South Kensington Campus London SW7 2AZ, UK.

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http://dx.doi.org/10.1002/minf.201400162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641463PMC
September 2015

The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease.

J Mol Biol 2015 Aug 11;427(17):2886-98. Epub 2015 Jul 11.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00222836150038
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http://dx.doi.org/10.1016/j.jmb.2015.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548493PMC
August 2015

The Phyre2 web portal for protein modeling, prediction and analysis.

Nat Protoc 2015 Jun 7;10(6):845-58. Epub 2015 May 7.

Structural Bioinformatics Group, Imperial College London, London, UK.

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http://dx.doi.org/10.1038/nprot.2015.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5298202PMC
June 2015

Partial protein domains: evolutionary insights and bioinformatics challenges.

Genome Biol 2015 May 19;16:100. Epub 2015 May 19.

Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1186/s13059-015-0663-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436111PMC
May 2015

SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features.

J Mol Biol 2014 Jul 5;426(14):2692-701. Epub 2014 May 5.

Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/j.jmb.2014.04.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4087249PMC
July 2014

The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions.

J Mol Biol 2013 Nov 15;425(21):3949-63. Epub 2013 Jul 15.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, South Kensington, SW7 2AZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2013.07.012DOI Listing
November 2013

Polyproline-II helix in proteins: structure and function.

J Mol Biol 2013 Jun 16;425(12):2100-32. Epub 2013 Mar 16.

Engelhard Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Street 32, Moscow 119991, Russia.

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http://dx.doi.org/10.1016/j.jmb.2013.03.018DOI Listing
June 2013

Proteins and domains vary in their tolerance of non-synonymous single nucleotide polymorphisms (nsSNPs).

J Mol Biol 2013 Apr 25;425(8):1274-86. Epub 2013 Jan 25.

Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/j.jmb.2013.01.026DOI Listing
April 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response.

BMC Syst Biol 2013 Mar 25;7:26. Epub 2013 Mar 25.

Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, SW7 2AZ, UK.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0
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http://dx.doi.org/10.1186/1752-0509-7-26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656802PMC
March 2013

Protein flexibility, not disorder, is intrinsic to molecular recognition.

F1000 Biol Rep 2013 11;5. Epub 2013 Jan 11.

Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris-Sud 91405-Orsay, France.

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http://dx.doi.org/10.3410/B5-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3542771PMC
January 2013

A new structural model of the acid-labile subunit: pathogenetic mechanisms of short stature-causing mutations.

J Mol Endocrinol 2012 Dec 12;49(3):213-20. Epub 2012 Oct 12.

Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1530/JME-12-0086DOI Listing
December 2012

CombFunc: predicting protein function using heterogeneous data sources.

Nucleic Acids Res 2012 Jul 27;40(Web Server issue):W466-70. Epub 2012 May 27.

Centre for Bioinformatics, Imperial College London, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1093/nar/gks489DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394346PMC
July 2012

Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study.

BMC Bioinformatics 2012 Jul 11;13:162. Epub 2012 Jul 11.

Computational Bioinformatics Laboratory, Department of Computer Science, Imperial College London, London, SW7 2BZ, UK.

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http://dx.doi.org/10.1186/1471-2105-13-162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458898PMC
July 2012

Assessment of a rule-based virtual screening technology (INDDEx) on a benchmark data set.

J Phys Chem B 2012 Jun 28;116(23):6732-9. Epub 2012 Mar 28.

Department of Life Science, Imperial College London, London, SW7 2AZ United Kingdom.

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http://dx.doi.org/10.1021/jp212084fDOI Listing
June 2012

PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction.

Bioinformatics 2012 May 13;28(9):1239-45. Epub 2012 Mar 13.

Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College, London, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338015PMC
May 2012

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs.

Hum Mutat 2012 Feb 27;33(2):359-63. Epub 2011 Dec 27.

Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1002/humu.21656DOI Listing
February 2012

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.

Authors:
John C Chambers Weihua Zhang Joban Sehmi Xinzhong Li Mark N Wass Pim Van der Harst Hilma Holm Serena Sanna Maryam Kavousi Sebastian E Baumeister Lachlan J Coin Guohong Deng Christian Gieger Nancy L Heard-Costa Jouke-Jan Hottenga Brigitte Kühnel Vinod Kumar Vasiliki Lagou Liming Liang Jian'an Luan Pedro Marques Vidal Irene Mateo Leach Paul F O'Reilly John F Peden Nilufer Rahmioglu Pasi Soininen Elizabeth K Speliotes Xin Yuan Gudmar Thorleifsson Behrooz Z Alizadeh Larry D Atwood Ingrid B Borecki Morris J Brown Pimphen Charoen Francesco Cucca Debashish Das Eco J C de Geus Anna L Dixon Angela Döring Georg Ehret Gudmundur I Eyjolfsson Martin Farrall Nita G Forouhi Nele Friedrich Wolfram Goessling Daniel F Gudbjartsson Tamara B Harris Anna-Liisa Hartikainen Simon Heath Gideon M Hirschfield Albert Hofman Georg Homuth Elina Hyppönen Harry L A Janssen Toby Johnson Antti J Kangas Ido P Kema Jens P Kühn Sandra Lai Mark Lathrop Markus M Lerch Yun Li T Jake Liang Jing-Ping Lin Ruth J F Loos Nicholas G Martin Miriam F Moffatt Grant W Montgomery Patricia B Munroe Kiran Musunuru Yusuke Nakamura Christopher J O'Donnell Isleifur Olafsson Brenda W Penninx Anneli Pouta Bram P Prins Inga Prokopenko Ralf Puls Aimo Ruokonen Markku J Savolainen David Schlessinger Jeoffrey N L Schouten Udo Seedorf Srijita Sen-Chowdhry Katherine A Siminovitch Johannes H Smit Timothy D Spector Wenting Tan Tanya M Teslovich Taru Tukiainen Andre G Uitterlinden Melanie M Van der Klauw Ramachandran S Vasan Chris Wallace Henri Wallaschofski H-Erich Wichmann Gonneke Willemsen Peter Würtz Chun Xu Laura M Yerges-Armstrong Goncalo R Abecasis Kourosh R Ahmadi Dorret I Boomsma Mark Caulfield William O Cookson Cornelia M van Duijn Philippe Froguel Koichi Matsuda Mark I McCarthy Christa Meisinger Vincent Mooser Kirsi H Pietiläinen Gunter Schumann Harold Snieder Michael J E Sternberg Ronald P Stolk Howard C Thomas Unnur Thorsteinsdottir Manuela Uda Gérard Waeber Nicholas J Wareham Dawn M Waterworth Hugh Watkins John B Whitfield Jacqueline C M Witteman Bruce H R Wolffenbuttel Caroline S Fox Mika Ala-Korpela Kari Stefansson Peter Vollenweider Henry Völzke Eric E Schadt James Scott Marjo-Riitta Järvelin Paul Elliott Jaspal S Kooner

Nat Genet 2011 Oct 16;43(11):1131-8. Epub 2011 Oct 16.

Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, UK.

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http://hmg.oxfordjournals.org/content/early/2012/09/04/hmg.d
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http://www.nature.com/doifinder/10.1038/ng.970
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http://dx.doi.org/10.1038/ng.970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482372PMC
October 2011

Functional significance of mutations in the Snf2 domain of ATRX.

Hum Mol Genet 2011 Jul 19;20(13):2603-10. Epub 2011 Apr 19.

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK.

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http://dx.doi.org/10.1093/hmg/ddr163DOI Listing
July 2011

Challenges for the prediction of macromolecular interactions.

Curr Opin Struct Biol 2011 Jun 14;21(3):382-90. Epub 2011 Apr 14.

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, South Kensington, London, UK.

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https://linkinghub.elsevier.com/retrieve/pii/S0959440X110006
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http://dx.doi.org/10.1016/j.sbi.2011.03.013DOI Listing
June 2011

Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe.

Bioinformatics 2010 Nov 15;26(21):2664-71. Epub 2010 Sep 15.

Department of Life Science, Imperial College London, London, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq527DOI Listing
November 2010

3DLigandSite: predicting ligand-binding sites using similar structures.

Nucleic Acids Res 2010 Jul 31;38(Web Server issue):W469-73. Epub 2010 May 31.

Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London, London, SW7 2AZ, UK.

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http://dx.doi.org/10.1093/nar/gkq406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896164PMC
July 2010

Genetic loci influencing kidney function and chronic kidney disease.

Authors:
John C Chambers Weihua Zhang Graham M Lord Pim van der Harst Debbie A Lawlor Joban S Sehmi Daniel P Gale Mark N Wass Kourosh R Ahmadi Stephan J L Bakker Jacqui Beckmann Henk J G Bilo Murielle Bochud Morris J Brown Mark J Caulfield John M C Connell H Terence Cook Ioana Cotlarciuc George Davey Smith Ranil de Silva Guohong Deng Olivier Devuyst Lambert D Dikkeschei Nada Dimkovic Mark Dockrell Anna Dominiczak Shah Ebrahim Thomas Eggermann Martin Farrall Luigi Ferrucci Jurgen Floege Nita G Forouhi Ron T Gansevoort Xijin Han Bo Hedblad Jaap J Homan van der Heide Bouke G Hepkema Maria Hernandez-Fuentes Elina Hypponen Toby Johnson Paul E de Jong Nanne Kleefstra Vasiliki Lagou Marta Lapsley Yun Li Ruth J F Loos Jian'an Luan Karin Luttropp Céline Maréchal Olle Melander Patricia B Munroe Louise Nordfors Afshin Parsa Leena Peltonen Brenda W Penninx Esperanza Perucha Anneli Pouta Inga Prokopenko Paul J Roderick Aimo Ruokonen Nilesh J Samani Serena Sanna Martin Schalling David Schlessinger Georg Schlieper Marc A J Seelen Alan R Shuldiner Marketa Sjögren Johannes H Smit Harold Snieder Nicole Soranzo Timothy D Spector Peter Stenvinkel Michael J E Sternberg Ramasamyiyer Swaminathan Toshiko Tanaka Lielith J Ubink-Veltmaat Manuela Uda Peter Vollenweider Chris Wallace Dawn Waterworth Klaus Zerres Gerard Waeber Nicholas J Wareham Patrick H Maxwell Mark I McCarthy Marjo-Riitta Jarvelin Vincent Mooser Goncalo R Abecasis Liz Lightstone James Scott Gerjan Navis Paul Elliott Jaspal S Kooner

Nat Genet 2010 May 11;42(5):373-5. Epub 2010 Apr 11.

Department of Epidemiology and Biostatistics, School of Public Health, Imperial College of London, London, UK.

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http://dx.doi.org/10.1038/ng.566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748585PMC
May 2010

Protein folding requires crowd control in a simulated cell.

J Mol Biol 2010 Apr 10;397(5):1329-38. Epub 2010 Feb 10.

Division of Molecular Biosciences, Biochemistry Building, Imperial College London, South Kensington, London SW7 2AZ, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S002228361000131
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http://dx.doi.org/10.1016/j.jmb.2010.01.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2891488PMC
April 2010

Prediction of ligand binding sites using homologous structures and conservation at CASP8.

Proteins 2009 ;77 Suppl 9:147-51

Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London, London SW7 2AZ, United Kingdom.

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http://dx.doi.org/10.1002/prot.22513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814558PMC
January 2010

Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB).

Bioinform Biol Insights 2009 Nov 24;1:77-90. Epub 2009 Nov 24.

Laboratori de Bioinformàtica, Institut de Biomedicina I Biotecnologia, Universitat Autònoma de Barcelona, Bellaterra 08193, Catalonia. Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789696PMC
November 2009

Discovering rules for protein-ligand specificity using support vector inductive logic programming.

Protein Eng Des Sel 2009 Sep 2;22(9):561-7. Epub 2009 Jul 2.

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London, UK.

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http://dx.doi.org/10.1093/protein/gzp035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913550PMC
September 2009

The fine details of evolution.

Biochem Soc Trans 2009 Aug;37(Pt 4):723-6

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1042/BST0370723DOI Listing
August 2009

Protein structure prediction on the Web: a case study using the Phyre server.

Nat Protoc 2009 ;4(3):363-71

Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK.

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http://dx.doi.org/10.1038/nprot.2009.2DOI Listing
April 2009

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking.

Proc Natl Acad Sci U S A 2008 Jul 18;105(30):10390-5. Epub 2008 Jul 18.

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0802496105
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475499PMC
July 2008

3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm.

Bioinformatics 2008 May 7;24(9):1137-44. Epub 2008 Mar 7.

Division of Molecular Biosciences, Imperial College London, South Kensington, London SW72AZ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn093DOI Listing
May 2008

Scaffold hopping in drug discovery using inductive logic programming.

J Chem Inf Model 2008 May 6;48(5):949-57. Epub 2008 May 6.

Computational Bioinformatics Laboratory, Department of Computing, Imperial College London, 180 Queen's Gate, London SW7 2AZ, United Kingdom.

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http://dx.doi.org/10.1021/ci700418fDOI Listing
May 2008

ConFunc--functional annotation in the twilight zone.

Bioinformatics 2008 Mar 8;24(6):798-806. Epub 2008 Feb 8.

Structural Bioinformatics Group, Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK.

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March 2008

Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.

Proteins 2008 Feb;70(3):611-25

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom.

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http://doi.wiley.com/10.1002/prot.21688
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February 2008

Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods.

J Proteome Res 2008 Feb 8;7(2):497-503. Epub 2008 Jan 8.

Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology & Anaesthetics, Sir Alexander Fleming Building, Imperial College, London SW7 2AZ, UK.

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http://dx.doi.org/10.1021/pr070350lDOI Listing
February 2008

A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.

Proteins 2007 Dec;69(4):823-31

Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom.

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http://doi.wiley.com/10.1002/prot.21782
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December 2007

A novel logic-based approach for quantitative toxicology prediction.

J Chem Inf Model 2007 May-Jun;47(3):998-1006. Epub 2007 Apr 24.

Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, and Computational Bioinformatics Laboratory, Department of Computing, Imperial College London, London SW7 2AZ, U.K.

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http://dx.doi.org/10.1021/ci600223dDOI Listing
September 2007

Convergent evolution of enzyme active sites is not a rare phenomenon.

J Mol Biol 2007 Sep 14;372(3):817-45. Epub 2007 Jun 14.

Biochemistry Building, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK.

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September 2007

The identification of similarities between biological networks: application to the metabolome and interactome.

J Mol Biol 2007 Jun 14;369(4):1126-39. Epub 2007 Mar 14.

Division of Molecular Biosciences, Imperial College London, South Kensington, London SW7 2AZ, UK.

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June 2007

Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds.

J Comput Aided Mol Des 2007 May 27;21(5):269-80. Epub 2007 Mar 27.

Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.

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http://dx.doi.org/10.1007/s10822-007-9113-3DOI Listing
May 2007

Prediction of viable circular permutants using a graph theoretic approach.

Bioinformatics 2006 Jun 16;22(11):1353-8. Epub 2006 Mar 16.

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btl095DOI Listing
June 2006

Capturing expert knowledge with argumentation: a case study in bioinformatics.

Bioinformatics 2006 Apr 29;22(8):924-33. Epub 2006 Jan 29.

Division of Molecular Biosciences, Imperial College, London SW7 2AZ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btl018DOI Listing
April 2006

Introduction. Bioinformatics: from molecules to systems.

Philos Trans R Soc Lond B Biol Sci 2006 Mar;361(1467):389-91

University College London Department of Computer Science, Bioinformatics Unit Gower Street, London WC1E 6BT, UK.

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http://dx.doi.org/10.1098/rstb.2005.1811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609343PMC
March 2006

The proteome: structure, function and evolution.

Philos Trans R Soc Lond B Biol Sci 2006 Mar;361(1467):441-51

Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609342PMC
March 2006

Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.

Proteins 2005 Sep;60(4):746-57

Institute of Biomedicine and Biotechnology, Universitat Autonoma de Barcelona, Bellaterra, Barcelona, Spain.

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September 2005

Isolation of a small molecule inhibitor of DNA base excision repair.

Nucleic Acids Res 2005 19;33(15):4711-24. Epub 2005 Aug 19.

Cancer Research UK Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford, OX3 9DS, UK.

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http://dx.doi.org/10.1093/nar/gki781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188083PMC
September 2005

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

J Mol Biol 2005 Sep;352(4):1002-15

Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK.

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September 2005

Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.

Proteins 2005 Aug;60(2):281-8

Department of Biological Sciences, Imperial College, London, United Kingdom.

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http://dx.doi.org/10.1002/prot.20571DOI Listing
August 2005

The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking.

J Mol Biol 2005 Apr;347(5):1077-101

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.

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April 2005

Automated prediction of protein function and detection of functional sites from structure.

Proc Natl Acad Sci U S A 2004 Oct 29;101(41):14754-9. Epub 2004 Sep 29.

Structural Bioinformatics Group, Biochemistry Building, Department of Biological Sciences, Imperial College London, London SW7 2AZ, UK.

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http://dx.doi.org/10.1073/pnas.0404569101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC522026PMC
October 2004

Analysis of phenetic trees based on metabolic capabilites across the three domains of life.

J Mol Biol 2004 Jul;340(3):491-512

Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.

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http://dx.doi.org/10.1016/j.jmb.2004.04.059DOI Listing
July 2004

Clustering of protein domains in the human genome.

J Mol Biol 2004 Jul;340(5):991-1004

Department of Epidemiology and Public Health, Imperial College, St Mary's Campus, London W2 1PG, UK.

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http://dx.doi.org/10.1016/j.jmb.2004.05.036DOI Listing
July 2004

ArchDB: automated protein loop classification as a tool for structural genomics.

Nucleic Acids Res 2004 Jan;32(Database issue):D185-8

Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1093/nar/gkh002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308737PMC
January 2004

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

Nucleic Acids Res 2004 Jan;32(Database issue):D245-50

Department of Biological Sciences and Centre for Bioinformatics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308798PMC
January 2004

CAPRI: a Critical Assessment of PRedicted Interactions.

Proteins 2003 Jul;52(1):2-9

Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.

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http://doi.wiley.com/10.1002/prot.10381
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July 2003

Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial.

Proteins 2003 Jul;52(1):74-9

Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London, United Kingdom.

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http://dx.doi.org/10.1002/prot.10396DOI Listing
July 2003

The automatic discovery of structural principles describing protein fold space.

J Mol Biol 2003 Jul;330(4):839-50

Cancer Research UK, Biomolecular Modelling Laboratory, 44 Lincoln's Inn Fields, London WC2A 3PX, UK.

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http://dx.doi.org/10.1016/s0022-2836(03)00620-xDOI Listing
July 2003

Structural characterization of the human proteome.

Genome Res 2002 Nov;12(11):1625-41

Biomolecular Modelling Laboratory, Cancer Research UK, London, United Kingdom.

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http://www.genome.org/cgi/doi/10.1101/gr.221202
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187559PMC
November 2002

Evolution of enzymes in metabolism: a network perspective.

J Mol Biol 2002 Jul;320(4):751-70

Department of Biological Sciences, Structural Bioinformatics Group, Biochemistry Building, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK.

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http://dx.doi.org/10.1016/s0022-2836(02)00546-6DOI Listing
July 2002

Modeling of protein interactions in genomes.

Proteins 2002 Jun;47(4):444-6

Biomedical Engineering, Boston University, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1002/prot.10112DOI Listing
June 2002

Prediction of protein-protein interactions by docking methods.

Curr Opin Struct Biol 2002 Feb;12(1):28-35

Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, 44 Lincoln's Inn Fields, WC2A 3PX, London, UK.

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February 2002