-
Je něco špatně v tomto záznamu ?
Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
PD. Adams, K. Aertgeerts, C. Bauer, JA. Bell, HM. Berman, TN. Bhat, JM. Blaney, E. Bolton, G. Bricogne, D. Brown, SK. Burley, DA. Case, KL. Clark, T. Darden, P. Emsley, VA. Feher, Z. Feng, CR. Groom, SF. Harris, J. Hendle, T. Holder, A....
Jazyk angličtina Země Spojené státy americké
Typ dokumentu kongresy, Research Support, N.I.H., Extramural, práce podpořená grantem
NLK
Cell Press Free Archives
od 1995-01-01 do Před 1 rokem
Free Medical Journals
od 1995 do Před 1 rokem
Free Medical Journals
od 1995 do Před 1 rokem
- MeSH
- databáze proteinů * MeSH
- datové kurátorství MeSH
- konformace proteinů MeSH
- krystalografie rentgenová MeSH
- ligandy MeSH
- molekulární modely MeSH
- proteiny chemie MeSH
- směrnice jako téma MeSH
- Publikační typ
- kongresy MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
Agios Pharmaceuticals Inc Cambridge MA 02139 USA
Astex Pharmaceuticals Cambridge CB4 0QA UK
BioMagResBank Department of Biochemistry University of Wisconsin Madison Madison WI 53706 1544 USA
Bioscience Division Los Alamos National Laboratory Los Alamos NM 87545 USA
Biosystems and Biomaterials Division NIST Gaithersburg MD 20899 USA
Bristol Myers Squibb Research and Development Pennington NJ 08534 USA
Bristol Myers Squibb Research and Development Princeton NJ 08543 USA
Bruker AXS Inc Madison WI 53711 USA
Cambridge Crystallographic Data Centre Cambridge CB2 1EZ UK
Charles River Ltd Structural Biology and Biophysics Cambridge CB10 1XL UK
DART NeuroScience LLC San Diego CA 92131 USA
Department of Biochemistry and Biophysics Oregon State University Corvallis OR 97331 USA
Genentech Inc South San Francisco CA 94080 USA
GlaxoSmithKline Collegeville PA 19426 USA
Global Phasing Ltd Cambridge CB3 0AX UK
Janssen Pharmaceuticals Inc Spring House PA 19002 USA
Merck Research Laboratories West Point PA 19486 USA
MRC Laboratory of Molecular Biology Cambridge CB2 0QH UK
National Center for Biotechnology Information U S National Library of Medicine Bethesda MD 20894 USA
Novartis Institutes for BioMedical Research Cambridge MA 02139 USA
OpenEye Scientific Cambridge MA 02142 USA
Protein Data Bank Japan Institute for Protein Research Osaka University Osaka 565 0871 Japan
School of Biosciences University of Kent Canterbury CT2 7NH UK
School of Chemistry and Molecular Biosciences University of Queensland St Lucia QLD 4072 Australia
Schrödinger Inc New York NY 10036 USA
Science For Solutions LLC West Windsor NJ 08550 USA
Structural Biology Center Biosciences Argonne National Laboratory Argonne IL 60439 USA
Structural Biology Lilly Biotechnology Center San Diego CA 92121 USA
Structural Genomics Consortium University of Oxford Oxford OX3 7DQ UK
Structural Genomics Consortium University of Toronto Toronto ON M5G 1L7 Canada
Citace poskytuje Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc17000294
- 003
- CZ-PrNML
- 005
- 20170117122306.0
- 007
- ta
- 008
- 170103s2016 xxu f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1016/j.str.2016.02.017 $2 doi
- 024 7_
- $a 10.1016/j.str.2016.02.017 $2 doi
- 035 __
- $a (PubMed)27050687
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a xxu
- 100 1_
- $a Adams, Paul D $u Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley Laboratory, Department of Bioengineering, UC Berkeley, Berkeley, CA 94720-8235, USA. $7 gn_A_00001600
- 245 10
- $a Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop / $c PD. Adams, K. Aertgeerts, C. Bauer, JA. Bell, HM. Berman, TN. Bhat, JM. Blaney, E. Bolton, G. Bricogne, D. Brown, SK. Burley, DA. Case, KL. Clark, T. Darden, P. Emsley, VA. Feher, Z. Feng, CR. Groom, SF. Harris, J. Hendle, T. Holder, A. Joachimiak, GJ. Kleywegt, T. Krojer, J. Marcotrigiano, AE. Mark, JL. Markley, M. Miller, W. Minor, GT. Montelione, G. Murshudov, A. Nakagawa, H. Nakamura, A. Nicholls, M. Nicklaus, RT. Nolte, AK. Padyana, CE. Peishoff, S. Pieniazek, RJ. Read, C. Shao, S. Sheriff, O. Smart, S. Soisson, J. Spurlino, T. Stouch, R. Svobodova, W. Tempel, TC. Terwilliger, D. Tronrud, S. Velankar, SC. Ward, GL. Warren, JD. Westbrook, P. Williams, H. Yang, J. Young,
- 520 9_
- $a Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
- 650 _2
- $a krystalografie rentgenová $7 D018360
- 650 _2
- $a datové kurátorství $7 D066289
- 650 12
- $a databáze proteinů $7 D030562
- 650 _2
- $a směrnice jako téma $7 D017408
- 650 _2
- $a ligandy $7 D008024
- 650 _2
- $a molekulární modely $7 D008958
- 650 _2
- $a konformace proteinů $7 D011487
- 650 _2
- $a proteiny $x chemie $7 D011506
- 655 _2
- $a kongresy $7 D016423
- 655 _2
- $a Research Support, N.I.H., Extramural $7 D052061
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Aertgeerts, Kathleen $u DART NeuroScience, LLC, San Diego, CA 92131, USA. $7 gn_A_00001954
- 700 1_
- $a Bauer, Cary $u Bruker AXS, Inc., Madison, WI 53711, USA.
- 700 1_
- $a Bell, Jeffrey A $u Schrödinger, Inc., New York, NY 10036, USA.
- 700 1_
- $a Berman, Helen M $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Bhat, Talapady N $u Biosystems and Biomaterials Division, NIST, Gaithersburg, MD 20899, USA.
- 700 1_
- $a Blaney, Jeff M $u Genentech, Inc., South San Francisco, CA 94080, USA.
- 700 1_
- $a Bolton, Evan $u National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA.
- 700 1_
- $a Bricogne, Gerard $u Global Phasing Ltd., Cambridge CB3 0AX, UK.
- 700 1_
- $a Brown, David $u School of Biosciences, University of Kent, Canterbury CT2 7NH, UK; Charles River Ltd., Structural Biology and Biophysics, Cambridge CB10 1XL, UK.
- 700 1_
- $a Burley, Stephen K $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: stephen.burley@rcsb.org.
- 700 1_
- $a Case, David A $u Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Clark, Kirk L $u Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
- 700 1_
- $a Darden, Tom $u OpenEye Scientific, Cambridge, MA 02142, USA.
- 700 1_
- $a Emsley, Paul $u MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
- 700 1_
- $a Feher, Victoria A $u Drug Design Data Resource and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: vfeher@ucsd.edu.
- 700 1_
- $a Feng, Zukang $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Groom, Colin R $u Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK. Electronic address: groom@ccdc.cam.ac.uk.
- 700 1_
- $a Harris, Seth F $u Genentech, Inc., South San Francisco, CA 94080, USA.
- 700 1_
- $a Hendle, Jorg $u Structural Biology, Lilly Biotechnology Center, San Diego, CA 92121, USA.
- 700 1_
- $a Holder, Thomas $u Schrödinger, Inc., New York, NY 10036, USA.
- 700 1_
- $a Joachimiak, Andrzej $u Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA.
- 700 1_
- $a Kleywegt, Gerard J $u Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
- 700 1_
- $a Krojer, Tobias $u Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.
- 700 1_
- $a Marcotrigiano, Joseph $u Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Mark, Alan E $u School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia.
- 700 1_
- $a Markley, John L $u BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA.
- 700 1_
- $a Miller, Matthew $u Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Minor, Wladek $u Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
- 700 1_
- $a Montelione, Gaetano T $u Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Murshudov, Garib $u MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
- 700 1_
- $a Nakagawa, Atsushi $u Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
- 700 1_
- $a Nakamura, Haruki $u Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
- 700 1_
- $a Nicholls, Anthony $u OpenEye Scientific, Cambridge, MA 02142, USA.
- 700 1_
- $a Nicklaus, Marc $u Computer-Aided Drug Design Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
- 700 1_
- $a Nolte, Robert T $u GlaxoSmithKline, Collegeville, PA 19426, USA.
- 700 1_
- $a Padyana, Anil K $u Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA.
- 700 1_
- $a Peishoff, Catherine E $u GlaxoSmithKline, Collegeville, PA 19426, USA.
- 700 1_
- $a Pieniazek, Susan $u Bristol-Myers Squibb Research and Development, Pennington, NJ 08534, USA.
- 700 1_
- $a Read, Randy J $u Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
- 700 1_
- $a Shao, Chenghua $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Sheriff, Steven $u Bristol-Myers Squibb Research and Development, Princeton, NJ 08543, USA.
- 700 1_
- $a Smart, Oliver $u Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
- 700 1_
- $a Soisson, Stephen $u Merck Research Laboratories, West Point, PA 19486, USA.
- 700 1_
- $a Spurlino, John $u Janssen Pharmaceuticals, Inc., Spring House, PA 19002, USA.
- 700 1_
- $a Stouch, Terry $u Science For Solutions, LLC, West Windsor, NJ 08550, USA.
- 700 1_
- $a Svobodova, Radka $u CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Brno, 625 00 Brno, Czech Republic.
- 700 1_
- $a Tempel, Wolfram $u Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.
- 700 1_
- $a Terwilliger, Thomas C $u Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- 700 1_
- $a Tronrud, Dale $u Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
- 700 1_
- $a Velankar, Sameer $u Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
- 700 1_
- $a Ward, Suzanna C $u Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK.
- 700 1_
- $a Warren, Gregory L $u OpenEye Scientific, Cambridge, MA 02142, USA.
- 700 1_
- $a Westbrook, John D $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Williams, Pamela $u Astex Pharmaceuticals, Cambridge CB4 0QA, UK.
- 700 1_
- $a Yang, Huanwang $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 700 1_
- $a Young, Jasmine $u Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
- 773 0_
- $w MED00006440 $t Structure (London, England 1993) $x 1878-4186 $g Roč. 24, č. 4 (2016), s. 502-8
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/27050687 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y a $z 0
- 990 __
- $a 20170103 $b ABA008
- 991 __
- $a 20170117122412 $b ABA008
- 999 __
- $a ok $b bmc $g 1179434 $s 960861
- BAS __
- $a 3
- BAS __
- $a PreBMC
- BMC __
- $a 2016 $b 24 $c 4 $d 502-8 $i 1878-4186 $m Structure $n Structure $x MED00006440
- LZP __
- $a Pubmed-20170103
