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BibTeX
DOT2: Macromolecular docking with improved biophysical models
Journal of computational chemistry, 2013-07, Vol.34 (20), p.1743-1758
Roberts, Victoria A.
Thompson, Elaine E.
Pique, Michael E.
Perez, Martin S.
Ten Eyck, L. F.
2013
Volltextzugriff (PDF)
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
Quelle
Wiley Online Library - AutoHoldings 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/.
Sprache
Englisch
Identifikatoren
ISSN: 0192-8651
eISSN: 1096-987X
DOI: 10.1002/jcc.23304
Titel-ID: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4370774
Format
–
Schlagworte
Algorithms
,
atomic solvation parameter
,
Biophysics
,
Computational Biology
,
Flexibility
,
Fourier analysis
,
Macromolecular Substances - chemistry
,
Molecular Docking Simulation
,
molecular recognition
,
Poisson-Boltzmann
,
protein-protein interactions
,
Proteins - chemistry
,
Software
,
Static Electricity
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