Roman Laskowski

Roman Laskowski

Senior Staff Scientist - Thornton research group

ORCID iD: 0000-0001-5528-0087

Tel:+44 (0)1223 492 542 / Fax:+44 (0)1223 494 468

Publications

2013

Abstracting knowledge from the protein data bank.
Furnham N, Laskowski RA, Thornton JM.
Biopolymers Volume 99 (2013) p.183-188
DOI: 10.1002/bip.22107

The Ramachandran plot and protein structure validation
Laskowski RA, Furnham N, Thornton JM.
Volume (2013) p.62-75
DOI: 10.1142/9789814449144_0005

2012

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM.
PLoS Comput Biol Volume 8 (2012) p.e1002403
DOI: 10.1371/journal.pcbi.1002403

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM.
Nucleic Acids Res Volume 40 (2012) p.d776-82
DOI: 10.1093/nar/gkr852

2011

Protein structure databases.
Laskowski RA.
Mol Biotechnol Volume 48 (2011) p.183-198
DOI: 10.1007/s12033-010-9372-4

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.
Hilton JM, Lewis MA, Grati M, Ingham N, Pearson S, Laskowski RA, Adams DJ, Steel KP.
Genome Biol Volume 12 (2011) p.r90
DOI: 10.1186/gb-2011-12-9-r90

1,000 structures and more from the MCSG.
Lee D, de Beer TA, Laskowski RA, Thornton JM, Orengo CA.
BMC Struct Biol Volume 11 (2011) p.2
DOI: 10.1186/1472-6807-11-2

Structural annotation of Mycobacterium tuberculosis proteome.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R, OSDD Consortium, Brahmachari SK, Chandra N.
PLoS One Volume 6 (2011) p.e27044
DOI: 10.1371/journal.pone.0027044

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
J Chem Inf Model Volume 51 (2011) p.2778-2786
DOI: 10.1021/ci200227u

2010

Protein structure databases.
Laskowski RA.
Methods Mol Biol Volume 609 (2010) p.59-82
DOI: 10.1007/978-1-60327-241-4_4

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA.
Bioinformatics Volume 26 (2010) p.1260-1261
DOI: 10.1093/bioinformatics/btq119

Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.
Nat Methods Volume 7 (2010) p.s42-55
DOI: 10.1038/nmeth.1427

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL.
J Med Chem Volume 53 (2010) p.3086-3094
DOI: 10.1021/jm901696w

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.
Proteins Volume 78 (2010) p.1120-1136
DOI: 10.1002/prot.22633

2009

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C.
Nat Genet Volume 41 (2009) p.1182-1190
DOI: 10.1038/ng.467

Integrated Servers for Structure-Informed Function Prediction
Laskowski RA.
Volume (2009) p.251-272
DOI: 10.1007/978-1-4020-9058-5_10

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.
PLoS Comput Biol Volume 5 (2009) p.e1000585
DOI: 10.1371/journal.pcbi.1000585

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochem Soc Trans Volume 37 (2009) p.723-726
DOI: 10.1042/bst0370723

PDBsum new things.
Laskowski RA.
Nucleic Acids Res Volume 37 (2009) p.d355-9
DOI: 10.1093/nar/gkn860

WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM.
Bioinformatics Volume 25 (2009) p.1192-1194
DOI: 10.1093/bioinformatics/btp116

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS Lett Volume 583 (2009) p.1692-1698
DOI: 10.1016/j.febslet.2009.03.019

2008

Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM.
Nat Rev Genet Volume 9 (2008) p.141-151
DOI: 10.1038/nrg2273

2007

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA.
Bioinformatics Volume 23 (2007) p.1824-1827
DOI: 10.1093/bioinformatics/btm085

The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
Proc Natl Acad Sci U S A Volume 104 (2007) p.5495-5500
DOI: 10.1073/pnas.0700800104

Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM.
J Mol Biol Volume 367 (2007) p.1511-1522
DOI: 10.1016/j.jmb.2007.01.063

Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
J Mol Biol Volume 368 (2007) p.283-301
DOI: 10.1016/j.jmb.2007.01.086

2006

A method for localizing ligand binding pockets in protein structures.
Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.
Proteins Volume 62 (2006) p.479-488
DOI: 10.1002/prot.20769

2005

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.w89-93
DOI: 10.1093/nar/gki414

Protein function prediction using local 3D templates.
Laskowski RA, Watson JD, Thornton JM.
J Mol Biol Volume 351 (2005) p.614-626
DOI: 10.1016/j.jmb.2005.05.067

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids.
Laskowski RA, Chistyakov VV, Thornton JM.
Nucleic Acids Res Volume 33 (2005) p.d266-8
DOI: 10.1093/nar/gki001

Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM.
Curr Opin Struct Biol Volume 15 (2005) p.275-284
DOI: 10.1016/j.sbi.2005.04.003

2004

X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution.
Savchenko A, Skarina T, Evdokimova E, Watson JD, Laskowski R, Arrowsmith CH, Edwards AM, Joachimiak A, Zhang RG.
Proteins Volume 54 (2004) p.162-165
DOI: 10.1002/prot.10585

2003

From protein structure to biochemical function?
Laskowski RA, Watson JD, Thornton JM.
J Struct Funct Genomics Volume 4 (2003) p.167-177
DOI: 10.1023/a:1026127927612

Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases.
Zhang RG, Duke N, Laskowski R, Evdokimova E, Skarina T, Edwards A, Joachimiak A, Savchenko A.
Proteins Volume 51 (2003) p.311-314
DOI: 10.1002/prot.10307

Estimation of weights and validation: a marginal likelihood approach.
Lebedev AA, Tickle IJ, Laskowski RA, Moss DS.
Acta Crystallogr D Biol Crystallogr Volume 59 (2003) p.1557-1566
DOI: 10.1107/s0907444903014367

Molecular basis of inherited diseases: a structural perspective.
Steward RE, MacArthur MW, Laskowski RA, Thornton JM.
Trends Genet Volume 19 (2003) p.505-513
DOI: 10.1016/s0168-9525(03)00195-1

Target selection and determination of function in structural genomics.
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM.
IUBMB Life Volume 55 (2003) p.249-255
DOI: 10.1080/1521654031000123385

2002

Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM.
Kim Y, Skarina T, Beasley S, Laskowski R, Arrowsmith C, Joachimiak A, Edwards A, Savchenko A.
Proteins Volume 48 (2002) p.427-430
DOI: 10.1002/prot.10160

Bioinformatics and protein design.
Laskowski RA, Chan AW.
Curr Pharm Biotechnol Volume 3 (2002) p.317-327
DOI: 10.2174/1389201023378157

2001

PDBsum: summaries and analyses of PDB structures.
Laskowski RA.
Nucleic Acids Res Volume 29 (2001) p.221-222
DOI: 10.1093/nar/29.1.221

1998

Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin.
Tickle IJ, Laskowski RA, Moss DS.
Acta Crystallogr D Biol Crystallogr Volume 54 (1998) p.243-252
DOI: 10.1107/s090744499701041x

Validation of protein models derived from experiment.
Laskowski RA, MacArthur MW, Thornton JM.
Curr Opin Struct Biol Volume 8 (1998) p.631-639
DOI: 10.1016/s0959-440x(98)80156-5

1997

PDBsum: a Web-based database of summaries and analyses of all PDB structures.
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM.
Trends Biochem Sci Volume 22 (1997) p.488-490
DOI: 10.1016/s0968-0004(97)01140-7

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Luscombe NM, Laskowski RA, Thornton JM.
Nucleic Acids Res Volume 25 (1997) p.4940-4945
DOI: 10.1093/nar/25.24.4940

1996

X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.
Laskowski RA, Thornton JM, Humblet C, Singh J.
J Mol Biol Volume 259 (1996) p.175-201
DOI: 10.1006/jmbi.1996.0311

Conformational analysis of pentapeptide sequences matching a proposed recognition motif for lysosomal degradation.
Gorinsky B, Laskowski RA, Lee DA, Bomford A.
Biochim Biophys Acta Volume 1293 (1996) p.243-253
DOI: 10.1016/0167-4838(95)00256-1

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.
Wallace AC, Laskowski RA, Thornton JM.
Protein Sci Volume 5 (1996) p.1001-1013
DOI: 10.1002/pro.5560050603

1995

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions.
Laskowski RA.
J Mol Graph Volume 13 (1995) p.323-30, 307-8
DOI: 10.1016/0263-7855(95)00073-9

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Wallace AC, Laskowski RA, Thornton JM.
Protein Eng Volume 8 (1995) p.127-134
DOI: 10.1093/protein/8.2.127

1993

Main-chain bond lengths and bond angles in protein structures.
Laskowski RA, Moss DS, Thornton JM.
J Mol Biol Volume 231 (1993) p.1049-1067
DOI: 10.1006/jmbi.1993.1351