Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

J 2016

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

ADAMS, Paul D.; Kathleen AERTGEERTS; Cary BAUER; Jeffrey A. BELL; Helen M. BERMAN et al.

Základní údaje

Originální název

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Autoři

ADAMS, Paul D.; Kathleen AERTGEERTS; Cary BAUER; Jeffrey A. BELL; Helen M. BERMAN; Talapady N. BHAT; Jeff M. BLANEY; Evan BOLTON; Gerard BRICOGNE; David BROWN; Stephen K. BURLEY; David A. CASE; Kirk L. CLARK; Tom DARDEN; Paul EMSLEY; Victoria A. FEHER; Zukang FENG; Colin R. GROOM; Seth F. HARRIS; Jorg HENDLE; Thomas HOLDER; Andrzej JOACHIMIAK; Gerard J. KLEYWEGT; Tobias KROJER; Joseph MARCOTRIGIANO; Alan E. MARK; John L. MARKLEY; Matthew MILLER; Wladek MINOR; Gaetano T. MONTELIONE; Garib MURSHUDOV; Atsushi NAKAGAWA; Haruki NAKAMURA; Anthony NICHOLLS; Marc NICKLAUS; Robet T. NOLTE; Anil K. PADYANA; Catherine E. PEISHOFF; Susan PIENIAZEK; Randy J. READ; Chenghua SHAO; Steven SHERIFF; Oliver SMART; Stephen SOISSON; John SPURLINO; Terry STOUCH; Radka SVOBODOVÁ VAŘEKOVÁ; Wolfram TEMPEL; Thomas C. TERWILLIGER; Dale TRONRUD; Sameer VELANKAR; Suzanna C. WARD; Gregory L. WARREN; John D. WESTBROOK; Pamela WILLIAMS; Huanwang YANG a Jasmine YOUNG

Vydání

Structure, CAMBRIDGE, CELL PRESS, 2016, 0969-2126

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.945

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/16:00093806

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

PROTEIN DATA-BANK; CAMBRIDGE STRUCTURAL DATABASE; ELECTRON-DENSITY; TASK-FORCE; INFORMATION; MACROMOLECULES; GENERATION; MOLECULES; TOOLS; PDB

Štítky

rivok

Změněno: 6. 3. 2017 17:33, Mgr. Eva Špillingová

Anotace

V originále

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, similar to 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.

Citovat

@article{1374814,
   author = {Adams, Paul D. and Aertgeerts, Kathleen and Bauer, Cary and Bell, Jeffrey A. and Berman, Helen M. and Bhat, Talapady N. and Blaney, Jeff M. and Bolton, Evan and Bricogne, Gerard and Brown, David and Burley, Stephen K. and Case, David A. and Clark, Kirk L. and Darden, Tom and Emsley, Paul and Feher, Victoria A. and Feng, Zukang and Groom, Colin R. and Harris, Seth F. and Hendle, Jorg and Holder, Thomas and Joachimiak, Andrzej and Kleywegt, Gerard J. and Krojer, Tobias and Marcotrigiano, Joseph and Mark, Alan E. and Markley, John L. and Miller, Matthew and Minor, Wladek and Montelione, Gaetano T. and Murshudov, Garib and Nakagawa, Atsushi and Nakamura, Haruki and Nicholls, Anthony and Nicklaus, Marc and Nolte, Robet T. and Padyana, Anil K. and Peishoff, Catherine E. and Pieniazek, Susan and Read, Randy J. and Shao, Chenghua and Sheriff, Steven and Smart, Oliver and Soisson, Stephen and Spurlino, John and Stouch, Terry and Svobodová Vařeková, Radka and Tempel, Wolfram and Terwilliger, Thomas C. and Tronrud, Dale and Velankar, Sameer and Ward, Suzanna C. and Warren, Gregory L. and Westbrook, John D. and Williams, Pamela and Yang, Huanwang and Young, Jasmine},
   article_location = {CAMBRIDGE},
   article_number = {4},
   doi = {https://doi.org/10.1016/j.str.2016.02.017},
   keywords = {PROTEIN DATA-BANK; CAMBRIDGE STRUCTURAL DATABASE; ELECTRON-DENSITY; TASK-FORCE; INFORMATION; MACROMOLECULES; GENERATION; MOLECULES; TOOLS; PDB},
   language = {eng},
   issn = {0969-2126},
   journal = {Structure},
   title = {Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop},
   url = {http://www.sciencedirect.com/science/article/pii/S0969212616000769},
   volume = {24},
   year = {2016}
}

TY  - JOUR
ID  - 1374814
AU  - Adams, Paul D. - Aertgeerts, Kathleen - Bauer, Cary - Bell, Jeffrey A. - Berman, Helen M. - Bhat, Talapady N. - Blaney, Jeff M. - Bolton, Evan - Bricogne, Gerard - Brown, David - Burley, Stephen K. - Case, David A. - Clark, Kirk L. - Darden, Tom - Emsley, Paul - Feher, Victoria A. - Feng, Zukang - Groom, Colin R. - Harris, Seth F. - Hendle, Jorg - Holder, Thomas - Joachimiak, Andrzej - Kleywegt, Gerard J. - Krojer, Tobias - Marcotrigiano, Joseph - Mark, Alan E. - Markley, John L. - Miller, Matthew - Minor, Wladek - Montelione, Gaetano T. - Murshudov, Garib - Nakagawa, Atsushi - Nakamura, Haruki - Nicholls, Anthony - Nicklaus, Marc - Nolte, Robet T. - Padyana, Anil K. - Peishoff, Catherine E. - Pieniazek, Susan - Read, Randy J. - Shao, Chenghua - Sheriff, Steven - Smart, Oliver - Soisson, Stephen - Spurlino, John - Stouch, Terry - Svobodová Vařeková, Radka - Tempel, Wolfram - Terwilliger, Thomas C. - Tronrud, Dale - Velankar, Sameer - Ward, Suzanna C. - Warren, Gregory L. - Westbrook, John D. - Williams, Pamela - Yang, Huanwang - Young, Jasmine
PY  - 2016
TI  - Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
JF  - Structure
VL  - 24
IS  - 4
SP  - 502-508
EP  - 502-508
PB  - CELL PRESS
SN  - 09692126
KW  - PROTEIN DATA-BANK
KW  - CAMBRIDGE STRUCTURAL DATABASE
KW  - ELECTRON-DENSITY
KW  - TASK-FORCE
KW  - INFORMATION
KW  - MACROMOLECULES
KW  - GENERATION
KW  - MOLECULES
KW  - TOOLS
KW  - PDB
UR  - http://www.sciencedirect.com/science/article/pii/S0969212616000769
L2  - http://www.sciencedirect.com/science/article/pii/S0969212616000769
N2  - 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, similar to 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.
ER  -

Přehled o publikaci