Roman A Laskowski

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc 1,000 structures and more from the MCSG
    David Lee
    Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    BMC Struct Biol 11:2. 2011
  2. ncbi request reprint Understanding the molecular machinery of genetics through 3D structures
    Roman A Laskowski
    European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nat Rev Genet 9:141-51. 2008
  3. doi request reprint Protein structure databases
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Mol Biotechnol 48:183-98. 2011
  4. pmc ProFunc: a server for predicting protein function from 3D structure
    Roman A Laskowski
    European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W89-93. 2005
  5. ncbi request reprint Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 23:1824-7. 2007
  6. pmc PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D266-8. 2005
  7. doi request reprint LigPlot+: multiple ligand-protein interaction diagrams for drug discovery
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    J Chem Inf Model 51:2778-86. 2011
  8. pmc PDBsum new things
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D355-9. 2009
  9. doi request reprint The structural basis of allosteric regulation in proteins
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    FEBS Lett 583:1692-8. 2009
  10. doi request reprint The fine details of evolution
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Biochem Soc Trans 37:723-6. 2009

Detail Information

Publications34

  1. pmc 1,000 structures and more from the MCSG
    David Lee
    Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    BMC Struct Biol 11:2. 2011
    ..Structures of unknown function have stimulated the development of methods for function prediction from structure...
  2. ncbi request reprint Understanding the molecular machinery of genetics through 3D structures
    Roman A Laskowski
    European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Nat Rev Genet 9:141-51. 2008
    ..Finally, we describe how structure determination is benefiting from the high-throughput technologies of the worldwide structural genomics projects...
  3. doi request reprint Protein structure databases
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Mol Biotechnol 48:183-98. 2011
    ..Beyond these there are a vast number of databases for the most specialized user, dealing with specific families, diseases, structural features and so on...
  4. pmc ProFunc: a server for predicting protein function from 3D structure
    Roman A Laskowski
    European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:W89-93. 2005
    ..It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally...
  5. ncbi request reprint Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 23:1824-7. 2007
    ..Usually the best source of this information is the original article describing it, and it is often possible to discern the key aspects of the structure from just one or two of the figures in that article...
  6. pmc PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 33:D266-8. 2005
    ..In the past year, the database has been significantly improved, in terms of both appearance and new content. Moreover, it has moved to its new address at http://www.ebi.ac.uk/thornton-srv/databases/pdbsum...
  7. doi request reprint LigPlot+: multiple ligand-protein interaction diagrams for drug discovery
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    J Chem Inf Model 51:2778-86. 2011
    ....
  8. pmc PDBsum new things
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D355-9. 2009
    ..Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure...
  9. doi request reprint The structural basis of allosteric regulation in proteins
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    FEBS Lett 583:1692-8. 2009
    ..Here we review how analyses of experimentally determined models of protein 3D structures, using either X-ray crystallography or NMR spectroscopy, have revealed some of the mechanisms involved...
  10. doi request reprint The fine details of evolution
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Biochem Soc Trans 37:723-6. 2009
    ..The talks reported on some of the insights into evolution which have been obtained from the study of protein sequences, structures and systems...
  11. pmc Towards fully automated structure-based function prediction in structural genomics: a case study
    James D Watson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 367:1511-22. 2007
    ..We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment...
  12. pmc Target selection and determination of function in structural genomics
    James D Watson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    IUBMB Life 55:249-55. 2003
    ....
  13. doi request reprint On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
    Proteins 78:1120-36. 2010
    ..The presented results highlight the complexities of molecular recognition and underline the challenges of computational structural biology in developing methods to detect these important subtleties...
  14. ncbi request reprint A method for localizing ligand binding pockets in protein structures
    Fabian Glaser
    European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    Proteins 62:479-88. 2006
    ..We also show that this approach works better for enzymes than for nonenzyme proteins...
  15. doi request reprint Protein structure databases
    Roman A Laskowski
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Methods Mol Biol 609:59-82. 2010
    ..Beyond these there are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on...
  16. ncbi request reprint Predicting protein function from sequence and structural data
    James D Watson
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Curr Opin Struct Biol 15:275-84. 2005
    ..Several automated servers that integrate evidence from multiple sources have been released this year and particular improvements have been seen with methods utilizing the Gene Ontology functional annotation schema...
  17. pmc PDBsum additions
    Tjaart A P de Beer
    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, Palacky University Olomouc, Tr 17 listopadu 12, 771 46 Olomouc, Czech Republic
    Nucleic Acids Res 42:D292-6. 2014
    ....
  18. pmc LigSearch: a knowledge-based web server to identify likely ligands for a protein target
    Tjaart A P de Beer
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, England
    Acta Crystallogr D Biol Crystallogr 69:2395-402. 2013
    ..LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch. ..
  19. ncbi request reprint From protein structure to biochemical function?
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Struct Funct Genomics 4:167-77. 2003
    ..Here we present three examples, using structures solved by the Midwest Center for Structural Genomics consortium, illustrating the strengths and weaknesses of current approaches...
  20. ncbi request reprint Shape variation in protein binding pockets and their ligands
    Abdullah Kahraman
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    J Mol Biol 368:283-301. 2007
    ..Additionally, we observe a "buffer zone" or a region of free space between the ligand and protein, which results in binding pockets being on average three times larger than the ligand that they bind...
  21. doi request reprint WSsas: a web service for the annotation of functional residues through structural homologues
    David Talavera
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 25:1192-4. 2009
    ..In addition, WSsas can supply information about the relevant functional atoms. The web service definition (WSDL) file and a Perl client are freely available at http://www.ebi.ac.uk/thornton-srv/databases/WSsas/...
  22. pmc Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies
    Nicholas Furnham
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 8:e1002403. 2012
    ..This reinforces the hypothesis that relatively few ancient enzymatic domain superfamilies were progenitors for most of the chemistry required for life...
  23. pmc FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
    Nicholas Furnham
    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D776-82. 2012
    ..The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree...
  24. ncbi request reprint Protein function prediction using local 3D templates
    Roman A Laskowski
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    J Mol Biol 351:614-26. 2005
    ..In all, the methodology provides a powerful new tool for function prediction to complement those already in use...
  25. pmc Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset
    Tjaart A P de Beer
    European Molecular Biology Laboratory, European Bioinformatics Institute EMBL EBI, Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, United Kingdom
    PLoS Comput Biol 9:e1003382. 2013
    ..More modelling of the mutational processes at the nucleotide level is needed, but these observations should contribute to an improved prediction of the effects of specific variants in humans. ..
  26. doi request reprint Abstracting knowledge from the protein data bank
    Nicholas Furnham
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Biopolymers 99:183-8. 2013
    ..Here, we describe how the focus of protein structural analysis has developed over the past 40 years. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 183-188, 2013...
  27. pmc Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice
    Jennifer M Hilton
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Genome Biol 12:R90. 2011
    ..Genetic studies suggest an inherited component, but few of the genes that contribute to this condition are known. Mouse mutants have contributed significantly to the identification of genes predisposing to otitis media..
  28. ncbi request reprint Bioinformatics and protein design
    Roman A Laskowski
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    Curr Pharm Biotechnol 3:317-27. 2002
    ..Some examples of these successes, which are available in the Protein Data Bank, are presented. They suggest that carefully designed protein therapeutics are a genuine prospect for the future...
  29. ncbi request reprint Molecular basis of inherited diseases: a structural perspective
    Robert E Steward
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Trends Genet 19:505-13. 2003
  30. ncbi request reprint Structural quality assurance
    Roman A Laskowski
    Department of Biochemistry and Molecular Biology, University College London, University of London, London, UK
    Methods Biochem Anal 44:273-303. 2003
  31. pmc Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli
    Ruslan Sanishvili
    Biosciences Division, Argonne National Laboratory, Argonne, Illinois, 60439, USA
    J Biol Chem 278:26039-45. 2003
    ..The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure...
  32. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  33. ncbi request reprint Detecting cryptically simple protein sequences using the SIMPLE algorithm
    M Mar Albà
    Grup de Recerca en Informàtica Biomèdica, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Spain
    Bioinformatics 18:672-8. 2002
    ..However, many of these regions are encoded by non-repetitive DNA sequences and may therefore result from selection acting on protein structure and/or function...
  34. ncbi request reprint Estimation of weights and validation: a marginal likelihood approach
    Andrey A Lebedev
    School of Crystallography, Birkbeck College, London WC1E 7HX, England
    Acta Crystallogr D Biol Crystallogr 59:1557-66. 2003
    ..There is a known true value for the overall scaling coefficient for distance variances in restrained refinement and therefore the (maximum-likelihood) estimator for this coefficient may be used as a validation statistic...