Publications by authors named "Roman A Laskowski"

59Publications

VarSite: Disease variants and protein structure.

Protein Sci 2020 01 27;29(1):111-119. Epub 2019 Oct 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://dx.doi.org/10.1002/pro.3746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933866PMC
January 2020

VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations.

Bioinformatics 2019 11;35(22):4854-4856

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853667PMC
November 2019

PDBsum: Structural summaries of PDB entries.

Protein Sci 2018 01 27;27(1):129-134. Epub 2017 Oct 27.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1002/pro.3289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734310PMC
January 2018

The ProFunc Function Prediction Server.

Methods Mol Biol 2017 ;1611:75-95

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

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http://dx.doi.org/10.1007/978-1-4939-7015-5_7DOI Listing
February 2018

Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.

J Mol Biol 2016 07 14;428(15):3131-46. Epub 2016 Jul 14.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981433PMC
July 2016

Rising levels of atmospheric oxygen and evolution of Nrf2.

Sci Rep 2016 06 14;6:27740. Epub 2016 Jun 14.

Department of Chemistry, King's College London, United Kingdom.

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http://dx.doi.org/10.1038/srep27740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4906274PMC
June 2016

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

Nucleic Acids Res 2016 07 5;44(W1):W416-23. Epub 2016 May 5.

School of Mechanical Engineering, Hanyang University, Korea

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http://dx.doi.org/10.1093/nar/gkw368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987919PMC
July 2016

Protein Structure Databases.

Methods Mol Biol 2016 ;1415:31-53

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

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http://dx.doi.org/10.1007/978-1-4939-3572-7_2DOI Listing
December 2017

Proteins: interaction at a distance.

IUCrJ 2015 Nov 30;2(Pt 6):609-10. Epub 2015 Oct 30.

European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1107/S2052252515020217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4645104PMC
November 2015

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.

J Chem Theory Comput 2015 Sep 6;11(9):4086-92. Epub 2015 Aug 6.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.5b00398DOI Listing
September 2015

BetaCavityWeb: a webserver for molecular voids and channels.

Nucleic Acids Res 2015 Jul 22;43(W1):W413-8. Epub 2015 Apr 22.

Vorononi Diagram Research Center, Hanyang University, Korea School of Mechanical Engineering, Hanyang University, Korea

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http://dx.doi.org/10.1093/nar/gkv360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489219PMC
July 2015

Anatomy of enzyme channels.

BMC Bioinformatics 2014 Nov 18;15:379. Epub 2014 Nov 18.

Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, Olomouc, 771 46, Czech Republic.

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http://dx.doi.org/10.1186/s12859-014-0379-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245731PMC
November 2014

CATH: comprehensive structural and functional annotations for genome sequences.

Nucleic Acids Res 2015 Jan 27;43(Database issue):D376-81. Epub 2014 Oct 27.

Institute of Structural and Molecular Biology, UCL, 636 Darwin Building, Gower Street, WC1E 6BT, UK.

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http://dx.doi.org/10.1093/nar/gku947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384018PMC
January 2015

BetaVoid: molecular voids via beta-complexes and Voronoi diagrams.

Proteins 2014 Sep 20;82(9):1829-49. Epub 2014 Mar 20.

Vorononi Diagram Research Center, Hanyang University, Korea.

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http://dx.doi.org/10.1002/prot.24537DOI Listing
September 2014

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

PLoS Comput Biol 2013 12;9(12):e1003382. Epub 2013 Dec 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861039PMC
August 2014

LigSearch: a knowledge-based web server to identify likely ligands for a protein target.

Acta Crystallogr D Biol Crystallogr 2013 Dec 19;69(Pt 12):2395-402. Epub 2013 Nov 19.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England.

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http://dx.doi.org/10.1107/S0907444913022294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852652PMC
December 2013

PDBsum additions.

Nucleic Acids Res 2014 Jan 22;42(Database issue):D292-6. Epub 2013 Oct 22.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1093/nar/gkt940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965036PMC
January 2014

Abstracting knowledge from the Protein Data Bank.

Biopolymers 2013 Mar 29;99(3):183-8. Epub 2012 Sep 29.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1002/bip.22107DOI Listing
March 2013

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Nucleic Acids Res 2012 Jan 17;40(Database issue):D776-82. Epub 2011 Oct 17.

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

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http://dx.doi.org/10.1093/nar/gkr852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245072PMC
January 2012

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.

J Chem Inf Model 2011 Oct 5;51(10):2778-86. Epub 2011 Oct 5.

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

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http://dx.doi.org/10.1021/ci200227uDOI Listing
October 2011

Protein structure databases.

Mol Biotechnol 2011 Jun;48(2):183-98

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

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http://dx.doi.org/10.1007/s12033-010-9372-4DOI Listing
June 2011

1,000 structures and more from the MCSG.

BMC Struct Biol 2011 Jan 10;11. Epub 2011 Jan 10.

Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

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http://dx.doi.org/10.1186/1472-6807-11-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024214PMC
January 2011

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.

J Chem Theory Comput 2010 Jul;6(7):2191-203

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, Prague, Czech Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 00 Prague, Czech Republic, Palacký University, Department of Physical Chemistry, Faculty of Science, tø. 17. listopadu 12, 771 46, Olomouc, Czech Republic, and EMBL Outstation - Hinxton, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1021/ct100007yDOI Listing
July 2010

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.

Bioinformatics 2010 May 17;26(9):1260-1. Epub 2010 Mar 17.

Division of Mathematical Biology, The National Institute for Medical Research, The Ridgeway, London, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq119DOI Listing
May 2010

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.

J Med Chem 2010 Apr;53(8):3086-94

Biological and Medicinal Chemistry Group, Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E6BT, U.K.

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http://dx.doi.org/10.1021/jm901696wDOI Listing
April 2010

Protein structure databases.

Methods Mol Biol 2010 ;609:59-82

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-60327-241-4_4DOI Listing
May 2010

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

PLoS Comput Biol 2009 Dec 4;5(12):e1000585. Epub 2009 Dec 4.

Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1000585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777313PMC
December 2009

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.

Proteins 2010 Apr;78(5):1120-36

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.

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http://doi.wiley.com/10.1002/prot.22633
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http://dx.doi.org/10.1002/prot.22633DOI Listing
April 2010

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.

Nat Genet 2009 Nov 11;41(11):1182-90. Epub 2009 Oct 11.

Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108459PMC
November 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

The structural basis of allosteric regulation in proteins.

FEBS Lett 2009 Jun 18;583(11):1692-8. Epub 2009 Mar 18.

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

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http://dx.doi.org/10.1016/j.febslet.2009.03.019DOI Listing
June 2009

WSsas: a web service for the annotation of functional residues through structural homologues.

Bioinformatics 2009 May 27;25(9):1192-4. Epub 2009 Feb 27.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp116DOI Listing
May 2009

PDBsum new things.

Nucleic Acids Res 2009 Jan 7;37(Database issue):D355-9. Epub 2008 Nov 7.

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

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http://dx.doi.org/10.1093/nar/gkn860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686501PMC
January 2009

Understanding the molecular machinery of genetics through 3D structures.

Nat Rev Genet 2008 Feb;9(2):141-51

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

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http://dx.doi.org/10.1038/nrg2273DOI Listing
February 2008

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.

Bioinformatics 2007 Jul 24;23(14):1824-7. Epub 2007 Mar 24.

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

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http://dx.doi.org/10.1093/bioinformatics/btm085DOI Listing
July 2007

Shape variation in protein binding pockets and their ligands.

J Mol Biol 2007 Apr 7;368(1):283-301. Epub 2007 Feb 7.

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

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http://dx.doi.org/10.1016/j.jmb.2007.01.086DOI Listing
April 2007

Towards fully automated structure-based function prediction in structural genomics: a case study.

J Mol Biol 2007 Apr 30;367(5):1511-22. Epub 2007 Jan 30.

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

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http://dx.doi.org/10.1016/j.jmb.2007.01.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566530PMC
April 2007

A method for localizing ligand binding pockets in protein structures.

Proteins 2006 Feb;62(2):479-88

European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1002/prot.20769DOI Listing
February 2006

Protein function prediction using local 3D templates.

J Mol Biol 2005 Aug;351(3):614-26

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

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http://dx.doi.org/10.1016/j.jmb.2005.05.067DOI Listing
August 2005

ProFunc: a server for predicting protein function from 3D structure.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W89-93

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

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http://dx.doi.org/10.1093/nar/gki414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160175PMC
July 2005

Predicting protein function from sequence and structural data.

Curr Opin Struct Biol 2005 Jun;15(3):275-84

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

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http://dx.doi.org/10.1016/j.sbi.2005.04.003DOI Listing
June 2005

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.

Nucleic Acids Res 2005 Jan;33(Database issue):D266-8

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

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http://dx.doi.org/10.1093/nar/gki001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539955PMC
January 2005

From protein structure to biochemical function?

J Struct Funct Genomics 2003 ;4(2-3):167-77

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

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http://dx.doi.org/10.1023/a:1026127927612DOI Listing
July 2004

Molecular basis of inherited diseases: a structural perspective.

Trends Genet 2003 Sep;19(9):505-13

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

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https://linkinghub.elsevier.com/retrieve/pii/S01689525030019
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http://dx.doi.org/10.1016/S0168-9525(03)00195-1DOI Listing
September 2003

Estimation of weights and validation: a marginal likelihood approach.

Acta Crystallogr D Biol Crystallogr 2003 Sep 19;59(Pt 9):1557-66. Epub 2003 Aug 19.

School of Crystallography, Birkbeck College, London WC1E 7HX, England.

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http://dx.doi.org/10.1107/s0907444903014367DOI Listing
September 2003

Target selection and determination of function in structural genomics.

IUBMB Life 2003 Apr-May;55(4-5):249-55

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

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http://doi.wiley.com/10.1080/1521654031000123385
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http://dx.doi.org/10.1080/1521654031000123385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366504PMC
March 2004

Structural quality assurance.

Methods Biochem Anal 2003 ;44:273-303

Department of Biochemistry and Molecular Biology, University College London, University of London, London, UK.

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April 2003

Bioinformatics and protein design.

Curr Pharm Biotechnol 2002 Dec;3(4):317-27

European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.2174/1389201023378157DOI Listing
December 2002

Detecting cryptically simple protein sequences using the SIMPLE algorithm.

Bioinformatics 2002 May;18(5):672-8

Grup de Recerca en Informatica Biomèdica, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/18.5.672DOI Listing
May 2002