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. (840 Spojené státy), Kathleen AERTGEERTS (840 Spojené státy), Cary BAUER (840 Spojené státy), Jeffrey A. BELL (840 Spojené státy), Helen M. BERMAN (840 Spojené státy), Talapady N. BHAT (840 Spojené státy), Jeff M. BLANEY (840 Spojené státy), Evan BOLTON (840 Spojené státy), Gerard BRICOGNE (826 Velká Británie a Severní Irsko), David BROWN (826 Velká Británie a Severní Irsko), Stephen K. BURLEY (840 Spojené státy), David A. CASE (840 Spojené státy), Kirk L. CLARK (840 Spojené státy), Tom DARDEN (840 Spojené státy), Paul EMSLEY (826 Velká Británie a Severní Irsko), Victoria A. FEHER (840 Spojené státy), Zukang FENG (840 Spojené státy), Colin R. GROOM (826 Velká Británie a Severní Irsko), Seth F. HARRIS (840 Spojené státy), Jorg HENDLE (840 Spojené státy), Thomas HOLDER (840 Spojené státy), Andrzej JOACHIMIAK (840 Spojené státy), Gerard J. KLEYWEGT (826 Velká Británie a Severní Irsko), Tobias KROJER (826 Velká Británie a Severní Irsko), Joseph MARCOTRIGIANO (840 Spojené státy), Alan E. MARK (36 Austrálie), John L. MARKLEY (840 Spojené státy), Matthew MILLER (36 Austrálie), Wladek MINOR (840 Spojené státy), Gaetano T. MONTELIONE (840 Spojené státy), Garib MURSHUDOV (840 Spojené státy), Atsushi NAKAGAWA (392 Japonsko), Haruki NAKAMURA (392 Japonsko), Anthony NICHOLLS (826 Velká Británie a Severní Irsko), Marc NICKLAUS (840 Spojené státy), Robet T. NOLTE (840 Spojené státy), Anil K. PADYANA (840 Spojené státy), Catherine E. PEISHOFF (840 Spojené státy), Susan PIENIAZEK (840 Spojené státy), Randy J. READ (826 Velká Británie a Severní Irsko), Chenghua SHAO (840 Spojené státy), Steven SHERIFF (840 Spojené státy), Oliver SMART (840 Spojené státy), Stephen SOISSON (840 Spojené státy), John SPURLINO (840 Spojené státy), Terry STOUCH (840 Spojené státy), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, garant, domácí), Wolfram TEMPEL (124 Kanada), Thomas C. TERWILLIGER (840 Spojené státy), Dale TRONRUD (840 Spojené státy), Sameer VELANKAR (826 Velká Británie a Severní Irsko), Suzanna C. WARD (840 Spojené státy), Gregory L. WARREN (826 Velká Británie a Severní Irsko), John D. WESTBROOK (840 Spojené státy), Pamela WILLIAMS (826 Velká Británie a Severní Irsko), Huanwang YANG (840 Spojené státy) a Jasmine YOUNG (840 Spojené státy)

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

Kód RIV

RIV/00216224:14740/16:00093806

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1016/j.str.2016.02.017

UT WoS

000373568700005

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

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. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. CAMBRIDGE: CELL PRESS, 2016, roč. 24, č. 4, s. 502-508. ISSN 0969-2126. Dostupné z: https://dx.doi.org/10.1016/j.str.2016.02.017.

@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 = {http://dx.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  -

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. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. \textit{Structure}. CAMBRIDGE: CELL PRESS, 2016, roč.~24, č.~4, s.~502-508. ISSN~0969-2126. Dostupné z: https://dx.doi.org/10.1016/j.str.2016.02.017.

Podrobný výpis o publikaci