Details

Autor(en) / Beteiligte

• Roberts, Victoria A.
• Thompson, Elaine E.
• Pique, Michael E.
• Perez, Martin S.
• Ten Eyck, L. F.

Titel

DOT2: Macromolecular docking with improved biophysical models

Ist Teil von

• Journal of computational chemistry, 2013-07, Vol.34 (20), p.1743-1758

Ort / Verlag

United States: Blackwell Publishing Ltd

Erscheinungsjahr

2013

Link zum Volltext

Quelle

Wiley-Blackwell Journals

Beschreibungen/Notizen

• 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. © 2013 Wiley Periodicals, Inc. DOT2 is a versatile and transparent software suite for macromolecular docking for biochemists. Docking with the biologically relevant models of unbound proteins can distinguish the correct complex as the major cluster among the most favorable configurations. DOT2 is open source software available at www.sdsc.edu/CCMS/DOT/.