SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design

Our main objective was to compile a data set of high-quality protein–fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved str...

Full description

Saved in:
Bibliographic Details
Published in:Journal of chemical information and modeling 2011-11, Vol.51 (11), p.2882-2896
Main Authors: Favia, Angelo D, Bottegoni, Giovanni, Nobeli, Irene, Bisignano, Paola, Cavalli, Andrea
Format: Article
Language:English
Subjects:
Algorithms
Animals
Applied sciences
Bacteria
Biological and medical sciences
Cluster Analysis
Computational Biology - methods
Computational Chemistry
Computer science
control theory
systems
Databases, Factual
Databases, Protein
Drug Discovery - methods
Exact sciences and technology
Fundamental and applied biological sciences. Psychology
Fungi
General pharmacology
Humans
Information systems. Data bases
Interactions. Associations
Intermolecular phenomena
Ligands
Medical sciences
Memory organisation. Data processing
Models, Molecular
Molecular biophysics
Pharmaceutical technology. Pharmaceutical industry
Pharmacology. Drug treatments
Physicochemical properties. Structure-activity relationships
Proteins
Protocol
Sampling
Software
Structure-Activity Relationship
Systems development
Thermodynamics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Our main objective was to compile a data set of high-quality protein–fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How thorough must the sampling be to replicate the experimental data? (iii) Can commonly used scoring functions discriminate between the native pose and other energy minima? The data set, named SERAPhiC (Selected Fragment Protein Complexes), is publicly available in a ready-to-dock format (http://www.iit.it/en/drug-discovery-and-development/seraphic.html). It offers computational medicinal chemists a reliable test set for both in silico protocol assessment and software development.
ISSN:1549-9596
1549-960X
DOI:10.1021/ci2003363