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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop
- Source :
- Structure (London, England : 1993), vol 24, iss 4, Adams, PD; Aertgeerts, K; Bauer, C; Bell, JA; Berman, HM; Bhat, TN; et al.(2016). Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure, 24(4), 502-508. doi: 10.1016/j.str.2016.02.017. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/42h5d920
- Publication Year :
- 2016
- Publisher :
- Elsevier BV, 2016.
-
Abstract
- Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent\ud an important source of information concerning drug-target interactions, providing atomic level insights\ud into the physical chemistry of complex formation between macromolecules and ligands. Of the\ud more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ~75% include at least one non-polymeric\ud ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug\ud discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across\ud the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic\ud Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop\ud held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015.\ud Experts in protein crystallography from academe and industry came together with non-profit and for-profit\ud software providers for crystallography and with experts in computational chemistry and data archiving to\ud discuss and make recommendations on best practices, as framed by a series of questions central to structural\ud studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived\ud in the PDB? How should the ligands be best represented? How should structural models of macromoleculeligand\ud complexes be validated? What supplementary information should accompany publications of structural\ud studies of biological macromolecules? Consensus recommendations on best practices developed in\ud response to each of these questions are provided, together with some details regarding implementation.\ud Important issues addressed but not resolved at the workshop are also enumerated.
- Subjects :
- 0301 basic medicine
Models, Molecular
Protein Conformation
Complex formation
Protein Data Bank (RCSB PDB)
Biophysics
Crystallographic data
Guidelines as Topic
010402 general chemistry
Crystallography, X-Ray
Ligands
01 natural sciences
Article
03 medical and health sciences
Structural bioinformatics
Databases
Extant taxon
Structural Biology
Models
Information and Computing Sciences
Databases, Protein
Molecular Biology
Data Curation
Crystallography
Ligand
Chemistry
Protein
Molecular
Proteins
computer.file_format
Collaboratory
Biological Sciences
Protein Data Bank
Data science
0104 chemical sciences
030104 developmental biology
Generic Health Relevance
QD431
Chemical Sciences
X-Ray
computer
Subjects
Details
- Language :
- English
- ISSN :
- 09692126
- Database :
- OpenAIRE
- Journal :
- Structure (London, England : 1993), vol 24, iss 4, Adams, PD; Aertgeerts, K; Bauer, C; Bell, JA; Berman, HM; Bhat, TN; et al.(2016). Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure, 24(4), 502-508. doi: 10.1016/j.str.2016.02.017. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/42h5d920
- Accession number :
- edsair.doi.dedup.....e2fa7fc51624930579bc888e19578253