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PMID: 19217386 Published · ppublish English Congress Research Support, N.I.H., Extramural

Outcome of a workshop on applications of protein models in biomedical research.

Structure (London, England : 1993) ·Vol. 17 ·No. 2 ·2009-02-13 ·Pages 151-9

Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA

Abstract

We describe the proceedings and conclusions from the "Workshop on Applications of Protein Models in Biomedical Research" (the Workshop) that was held at the University of California, San Francisco on 11 and 12 July, 2008. At the Workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) the requirements and challenges for different applications, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.

MeSH Terms
Animals Biomedical Research/methods,trends Chemistry, Pharmaceutical/methods Databases, Protein Drug Discovery/methods Enzymes/chemistry Health Planning Guidelines Humans Models, Molecular Protein Conformation Protein Engineering/methods Protein Interaction Mapping/methods Proteins/chemistry Software
Chemicals
Enzymes Proteins
Authors & Affiliations
32 authors, click to expand affiliations / ORCID
Schwede Torsten
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland. torsten.schwede@unibas.ch
Sali Andrej
Honig Barry
Levitt Michael
Berman Helen M
Jones David
Brenner Steven E
Burley Stephen K
Das Rhiju
Dokholyan Nikolay V
Dunbrack Roland L
Fidelis Krzysztof
Fiser Andras
Godzik Adam
Huang Yuanpeng Janet
Humblet Christine
Jacobson Matthew P
Joachimiak Andrzej
Krystek Stanley R
Kortemme Tanja
Kryshtafovych Andriy
Montelione Gaetano T
Moult John
Murray Diana
Sanchez Roberto
Sosnick Tobin R
Standley Daron M
Stouch Terry
Vajda Sandor
Vasquez Max
Westbrook John D
Wilson Ian A
References (97)
97 references, click to expand
  1. Functional impact of missense variants in BRCA1 predicted by supervised learning.
    PLoS Comput Biol. 2007 Feb 16;3(2):e26 PMID: 17305420
  2. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA.
    Dev Cell. 2005 Jan;8(1):19-30 PMID: 15621527
  3. Engineered antibody Fc variants with enhanced effector function.
    Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4005-10 PMID: 16537476
  4. The impact of structural genomics: expectations and outcomes.
    Science. 2006 Jan 20;311(5759):347-51 PMID: 16424331
  5. Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.
    Mol Microbiol. 2008 Jun;68(6):1395-405 PMID: 18452512
  6. CDART: protein homology by domain architecture.
    Genome Res. 2002 Oct;12(10):1619-23 PMID: 12368255
  7. Structure of a human ASF1a-HIRA complex and insights into specificity of histone chaperone complex assembly.
    Nat Struct Mol Biol. 2006 Oct;13(10):921-9 PMID: 16980972
  8. A humanized antibody that binds to the interleukin 2 receptor.
    Proc Natl Acad Sci U S A. 1989 Dec;86(24):10029-33 PMID: 2513570
  9. Protein structure determination from NMR chemical shifts.
    Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9615-20 PMID: 17535901
  10. Modeling of protein binary complexes using structural mass spectrometry data.
    Protein Sci. 2008 Jan;17(1):79-94 PMID: 18042684
  11. Protein structure prediction: inroads to biology.
    Mol Cell. 2005 Dec 22;20(6):811-9 PMID: 16364908
  12. Announcing the worldwide Protein Data Bank.
    Nat Struct Biol. 2003 Dec;10(12):980 PMID: 14634627
  13. Targeting the human cancer pathway protein interaction network by structural genomics.
    Mol Cell Proteomics. 2008 Oct;7(10):2048-60 PMID: 18487680
  14. Assessing model accuracy using the homology modeling automatically software.
    Proteins. 2008 Jan 1;70(1):105-18 PMID: 17640066
  15. Integrating diverse data for structure determination of macromolecular assemblies.
    Annu Rev Biochem. 2008;77:443-77 PMID: 18318657
  16. Assessment of CASP7 predictions for template-based modeling targets.
    Proteins. 2007;69 Suppl 8:38-56 PMID: 17894352
  17. Identification of a chloride ion binding site in Na+/Cl -dependent transporters.
    Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12761-6 PMID: 17652169
  18. Drug evaluation: PRX-00023, a selective 5-HT1A receptor agonist for depression.
    Curr Opin Investig Drugs. 2007 Jan;8(1):78-86 PMID: 17263189
  19. Regulation of the oxidative stress response through Slt2p-dependent destruction of cyclin C in Saccharomyces cerevisiae.
    Genetics. 2006 Mar;172(3):1477-86 PMID: 16387872
  20. Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle.
    Structure. 2005 Oct;13(10):1521-31 PMID: 16216583
  21. Comparative protein structure modeling of genes and genomes.
    Annu Rev Biophys Biomol Struct. 2000;29:291-325 PMID: 10940251
  22. A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists.
    J Am Chem Soc. 2008 Apr 16;130(15):5115-23 PMID: 18357984
  23. Characterizing the 1,4-dihydropyridines binding interactions in the L-type Ca2+ channel: model construction and docking calculations.
    J Med Chem. 2007 Apr 5;50(7):1504-13 PMID: 17335186
  24. Computational design of antibody-affinity improvement beyond in vivo maturation.
    Nat Biotechnol. 2007 Oct;25(10):1171-6 PMID: 17891135
  25. Analysis of KIT mutations in sporadic and familial gastrointestinal stromal tumors: therapeutic implications through protein modeling.
    Clin Cancer Res. 2005 May 15;11(10):3668-77 PMID: 15897563
  26. Kinases, homology models, and high throughput docking.
    J Med Chem. 2003 Oct 23;46(22):4638-47 PMID: 14561083
  27. Can correct protein models be identified?
    Protein Sci. 2003 May;12(5):1073-86 PMID: 12717029
  28. Engineered human IgG antibodies with longer serum half-lives in primates.
    J Biol Chem. 2004 Feb 20;279(8):6213-6 PMID: 14699147
  29. High-resolution structure prediction and the crystallographic phase problem.
    Nature. 2007 Nov 8;450(7167):259-64 PMID: 17934447
  30. Genome-wide analysis of membrane targeting by S. cerevisiae pleckstrin homology domains.
    Mol Cell. 2004 Mar 12;13(5):677-88 PMID: 15023338
  31. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor.
    Nature. 2007 Nov 15;450(7168):383-7 PMID: 17952055
  32. Statistical potential for assessment and prediction of protein structures.
    Protein Sci. 2006 Nov;15(11):2507-24 PMID: 17075131
  33. The molecular architecture of the nuclear pore complex.
    Nature. 2007 Nov 29;450(7170):695-701 PMID: 18046406
  34. 3D-Jury: a simple approach to improve protein structure predictions.
    Bioinformatics. 2003 May 22;19(8):1015-8 PMID: 12761065
  35. A semiempirical free energy force field with charge-based desolvation.
    J Comput Chem. 2007 Apr 30;28(6):1145-52 PMID: 17274016
  36. Fold recognition methods.
    Methods Biochem Anal. 2003;44:525-46 PMID: 12647403
  37. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes.
    Biochemistry. 2005 Feb 15;44(6):2059-71 PMID: 15697231
  38. Rational design of potent sialidase-based inhibitors of influenza virus replication.
    Nature. 1993 Jun 3;363(6428):418-23 PMID: 8502295
  39. A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.
    Nat Genet. 2008 Oct;40(10):1204-10 PMID: 18758461
  40. Predicting substrates by docking high-energy intermediates to enzyme structures.
    J Am Chem Soc. 2006 Dec 13;128(49):15882-91 PMID: 17147401
  41. Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data.
    Proc Natl Acad Sci U S A. 2007 May 8;104(19):7910-5 PMID: 17470807
  42. MODBASE: a database of annotated comparative protein structure models and associated resources.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5 PMID: 16381869
  43. Protein structure prediction servers at University College London.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W36-8 PMID: 15980489
  44. Protein structure fitting and refinement guided by cryo-EM density.
    Structure. 2008 Feb;16(2):295-307 PMID: 18275820
  45. Outcome of a workshop on archiving structural models of biological macromolecules.
    Structure. 2006 Aug;14(8):1211-7 PMID: 16955948
  46. The consensus coding sequences of human breast and colorectal cancers.
    Science. 2006 Oct 13;314(5797):268-74 PMID: 16959974
  47. Progress from CASP6 to CASP7.
    Proteins. 2007;69 Suppl 8:194-207 PMID: 17918728
  48. Macromolecular modeling with rosetta.
    Annu Rev Biochem. 2008;77:363-82 PMID: 18410248
  49. Combining X-ray crystallography and electron microscopy.
    Structure. 2005 Mar;13(3):355-62 PMID: 15766536
  50. Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion.
    Nat Genet. 2007 Jun;39(6):776-80 PMID: 17486094
  51. Loss of protein structure stability as a major causative factor in monogenic disease.
    J Mol Biol. 2005 Oct 21;353(2):459-73 PMID: 16169011
  52. Oligomerization of BAK by p53 utilizes conserved residues of the p53 DNA binding domain.
    J Biol Chem. 2008 Jul 25;283(30):21294-304 PMID: 18524770
  53. The role of molecular modelling in biomedical research.
    FEBS Lett. 2006 May 22;580(12):2928-34 PMID: 16647064
  54. Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer.
    Nat Genet. 2008 Jun;40(6):703-6 PMID: 18438407
  55. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
    Science. 2007 Nov 23;318(5854):1258-65 PMID: 17962520
  56. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme.
    J Mol Biol. 1969 May 28;42(1):65-86 PMID: 5817651
  57. The molecular sociology of the cell.
    Nature. 2007 Dec 13;450(7172):973-82 PMID: 18075576
  58. Novel leverage of structural genomics.
    Nat Biotechnol. 2007 Aug;25(8):849-51 PMID: 17687356
  59. Mechanism of membrane binding of the phospholipase D1 PX domain.
    J Biol Chem. 2004 Dec 24;279(52):54918-26 PMID: 15475361
  60. From virtuality to reality - Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective.
    Curr Opin Drug Discov Devel. 2008 Jul;11(4):559-68 PMID: 18600572
  61. SWISS-MODEL: An automated protein homology-modeling server.
    Nucleic Acids Res. 2003 Jul 1;31(13):3381-5 PMID: 12824332
  62. Harnessing knowledge from structural genomics.
    Structure. 2008 Jan;16(1):16-8 PMID: 18184578
  63. Prediction in 1D: secondary structure, membrane helices, and accessibility.
    Methods Biochem Anal. 2003;44:559-87 PMID: 12647405
  64. Structure-based activity prediction for an enzyme of unknown function.
    Nature. 2007 Aug 16;448(7155):775-9 PMID: 17603473
  65. The molecular basis of the differential subcellular localization of FYVE domains.
    J Biol Chem. 2004 Dec 17;279(51):53818-27 PMID: 15452113
  66. CAPRI: a Critical Assessment of PRedicted Interactions.
    Proteins. 2003 Jul 1;52(1):2-9 PMID: 12784359
  67. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
    J Med Chem. 2008 Apr 24;51(8):2502-11 PMID: 18333608
  68. IRAK-4 inhibitors. Part II: a structure-based assessment of imidazo[1,2-a]pyridine binding.
    Bioorg Med Chem Lett. 2008 Jun 1;18(11):3291-5 PMID: 18482836
  69. Computational docking and solution x-ray scattering predict a membrane-interacting role for the histone domain of the Ras activator son of sevenless.
    Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16632-7 PMID: 16267129
  70. Engineered enzymes for improved organic synthesis.
    Curr Opin Biotechnol. 2003 Aug;14(4):395-400 PMID: 12943848
  71. The PDB format, mmCIF, and other data formats.
    Methods Biochem Anal. 2003;44:161-79 PMID: 12647386
  72. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.
    Proc Natl Acad Sci U S A. 1951 Apr;37(4):205-11 PMID: 14816373
  73. Humanization of an anti-p185HER2 antibody for human cancer therapy.
    Proc Natl Acad Sci U S A. 1992 May 15;89(10):4285-9 PMID: 1350088
  74. Protein kinase inhibitors: insights into drug design from structure.
    Science. 2004 Mar 19;303(5665):1800-5 PMID: 15031492
  75. Recognition of errors in three-dimensional structures of proteins.
    Proteins. 1993 Dec;17(4):355-62 PMID: 8108378
  76. QMEAN: A comprehensive scoring function for model quality assessment.
    Proteins. 2008 Apr;71(1):261-77 PMID: 17932912
  77. ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
    Bioinformatics. 2004 Jan 1;20(1):45-50 PMID: 14693807
  78. Structure of a beta1-adrenergic G-protein-coupled receptor.
    Nature. 2008 Jul 24;454(7203):486-91 PMID: 18594507
  79. The cold-active lipase of Pseudomonas fragi. Heterologous expression, biochemical characterization and molecular modeling.
    Eur J Biochem. 2002 Jul;269(13):3321-8 PMID: 12084074
  80. An overview of the CCP4 project in protein crystallography: an example of a collaborative project.
    J Synchrotron Radiat. 2003 Jan 1;10(Pt 1):23-5 PMID: 12511787
  81. Humanization of an anti-vascular endothelial growth factor monoclonal antibody for the therapy of solid tumors and other disorders.
    Cancer Res. 1997 Oct 15;57(20):4593-9 PMID: 9377574
  82. High-resolution structure determination of the CylR2 homodimer using paramagnetic relaxation enhancement and structure-based prediction of molecular alignment.
    J Biomol NMR. 2008 Jan;40(1):1-13 PMID: 18026911
  83. Structure selection for protein kinase docking and virtual screening: homology models or crystal structures?
    Curr Protein Pept Sci. 2006 Oct;7(5):437-57 PMID: 17073695
  84. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller.
    Proteins. 2003;53 Suppl 6:534-41 PMID: 14579343
  85. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D230-4 PMID: 14681401
  86. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
    Structure. 2008 Nov 12;16(11):1668-77 PMID: 19000819
  87. Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
    Nat Chem Biol. 2007 Aug;3(8):486-91 PMID: 17603539
  88. Membrane targeting of C2 domains of phospholipase C-delta isoforms.
    J Biol Chem. 2002 Feb 1;277(5):3568-75 PMID: 11706040
  89. Determining the architectures of macromolecular assemblies.
    Nature. 2007 Nov 29;450(7170):683-94 PMID: 18046405
  90. Biochemical characterization of rous sarcoma virus MA protein interaction with membranes.
    J Virol. 2005 May;79(10):6227-38 PMID: 15858007
  91. Improving sequence-based fold recognition by using 3D model quality assessment.
    Bioinformatics. 2005 Sep 1;21(17):3509-15 PMID: 15955780
  92. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
    Nature. 1953 Apr 25;171(4356):737-8 PMID: 13054692
  93. Consistent blind protein structure generation from NMR chemical shift data.
    Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4685-90 PMID: 18326625
  94. Performance of 3D-database molecular docking studies into homology models.
    J Med Chem. 2004 Jan 29;47(3):764-7 PMID: 14736258
  95. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B.
    J Med Chem. 2002 May 23;45(11):2213-21 PMID: 12014959
  96. Docking and scoring protein complexes: CAPRI 3rd Edition.
    Proteins. 2007 Dec 1;69(4):704-18 PMID: 17918726
  97. Mutational analysis of the endothelin type A receptor (ETA): interactions and model of selective ETA antagonist BMS-182874 with putative ETA receptor binding cavity.
    Biochemistry. 1996 Feb 27;35(8):2548-56 PMID: 8611558
Article Info
Journal
Structure (London, England : 1993)
Abbr.
Structure
ISSN
0969-2126
DOI
10.1016/j.str.2008.12.014
Email
torsten.schwede@unibas.ch
Published
2009-02-13
Pages
151-9
Language
English
Region
United States
NLM ID
101087697
PMCID
PMC2739730
Subset
IM
Grants
NIGMS NIH HHS · U54 GM074958-04S2 · United States
NIGMS NIH HHS · R01 GM081642-02 · United States
NIGMS NIH HHS · R01 GM061867 · United States
NIGMS NIH HHS · P20 GM076222 · United States
NIGMS NIH HHS · P20 GM076222-02S1 · United States
NIGMS NIH HHS · R01 GM063817 · United States
NIGMS NIH HHS · R01 GM061867-09 · United States
NIGMS NIH HHS · R01 GM081642 · United States
NIGMS NIH HHS · U54 GM074958 · United States
NIGMS NIH HHS · R01 GM064700 · United States
NIGMS NIH HHS · U54 GM074942-04S2 · United States
NLM NIH HHS · P41 LM007085 · United States
NIGMS NIH HHS · R01 GM081642-01 · United States
NIGMS NIH HHS · R01 GM064700-08 · United States
NIGMS NIH HHS · U54 GM074942 · United States
External Links
PubMed source DOI: 10.1016/j.str.2008.12.014 PMC Full Text View journal details
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