DOT2: Macromolecular docking with improved biophysical models.
J Comput Chem
; 34(20): 1743-58, 2013 Jul 30.
Article
de En
| MEDLINE
| ID: mdl-23695987
ABSTRACT
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Logiciel
/
Protéines
/
Biologie informatique
/
Simulation de docking moléculaire
Type d'étude:
Prognostic_studies
Langue:
En
Journal:
J Comput Chem
Sujet du journal:
QUIMICA
Année:
2013
Type de document:
Article
Pays d'affiliation:
États-Unis d'Amérique