Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach.
Amino Acid Sequence
Benchmarking
Binding Sites
Carbohydrates
/ chemistry
Humans
Ligands
Molecular Docking Simulation
Peptides
/ chemistry
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Protein Interaction Mapping
Protein Multimerization
Proteins
/ chemistry
Research Design
Software
Structural Homology, Protein
Thermodynamics
docking minimization
elastic network model
induced fit
protein-protein complex formation
protein-protein interaction
Journal
Proteins
ISSN: 1097-0134
Titre abrégé: Proteins
Pays: United States
ID NLM: 8700181
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
15
09
2019
revised:
20
11
2019
accepted:
27
11
2019
pubmed:
1
12
2019
medline:
26
1
2021
entrez:
1
12
2019
Statut:
ppublish
Résumé
The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.
Substances chimiques
Carbohydrates
0
Ligands
0
Peptides
0
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1018-1028Informations de copyright
© 2019 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals, Inc.
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