相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
Ali May et al.
BIOINFORMATICS (2014)
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
Fabio Sterpone et al.
CHEMICAL SOCIETY REVIEWS (2014)
Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody-Antigen Complexes
Gautier Robin et al.
JOURNAL OF MOLECULAR BIOLOGY (2014)
Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation
Fabio Sterpone et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
Shruthi Viswanath et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2013)
Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective
Krishnakumar M. Ravikumar et al.
BIOPHYSICAL JOURNAL (2012)
The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins
Yassmine Chebaro et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Energy design for protein-protein interactions
D. V. S. Ravikant et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library
Brian G. Pierce et al.
PLOS ONE (2011)
Integrating atom-based and residue-based scoring functions for protein-protein docking
Thom Vreven et al.
PROTEIN SCIENCE (2011)
Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem
Richard M. Jackson
PROTEIN SCIENCE (2010)
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19
Howook Hwang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Protein-protein docking benchmark version 4.0
Howook Hwang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Designing coarse grained-and atom based-potentials for protein-protein docking
Dror Tobi
BMC STRUCTURAL BIOLOGY (2010)
FRODOCK: a new approach for fast rotational protein-protein docking
Jose Ignacio Garzon et al.
BIOINFORMATICS (2009)
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock et al.
BIOINFORMATICS (2009)
Generic coarse-grained model for protein folding and aggregation
Tristan Bereau et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
DOCKGROUND protein-protein docking decoy set
Shiyong Liu et al.
BIOINFORMATICS (2008)
The MARTINI coarse-grained force field: Extension to proteins
Luca Monticelli et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding
Young C. Kim et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
A combination of rescoring and refinement significantly improves protein docking performance
Brian Pierce et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)
A coarse-grained protein force field for folding and structure prediction
Julien Maupetit et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
ZRANK: Reranking protein docking predictions with an optimized energy function
Brian Pierce et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
Coarse-grained peptide modeling using a systematic multiscale approach
Jian Zhou et al.
BIOPHYSICAL JOURNAL (2007)
PIPER: An FFT-based protein docking program with pairwise potentials
Dima Kozakov et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Optimal clustering for detecting near-native conformations in protein docking
D Kozakov et al.
BIOPHYSICAL JOURNAL (2005)
Assessing predictions of protein-protein interaction: The CAPRI experiment
J Janin
PROTEIN SCIENCE (2005)
ClusPro: An automated docking and discrimination method for the prediction of protein complexes
SR Comeau et al.
BIOINFORMATICS (2004)
RDOCK: Refinement of rigid-body protein docking predictions
L Li et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
JJ Gray et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Assessment of blind predictions of protein-protein interactions:: Current status of docking methods
R Méndez et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
ICM-DISCO docking by global energy optimization with fully flexible side-chains
J Fernández-Recio et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
ZDOCK: An initial-stage protein-docking algorithm
R Chen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
M Zacharias
PROTEIN SCIENCE (2003)
A novel shape complementarity scoring function for protein-protein docking
R Chen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
R Chen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)