Refining multimeric protein complexes using conservation, electrostatics and probabilistic selection
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[1] A J Olson,et al. Structural symmetry and protein function. , 2000, Annual review of biophysics and biomolecular structure.
[2] Amarda Shehu,et al. Refinement of docked protein complex structures using evolutionary traces , 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).
[3] B. Donald,et al. Structure determination of symmetric homo‐oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing , 2006, Proteins.
[4] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[5] O. Lichtarge,et al. A family of evolution-entropy hybrid methods for ranking protein residues by importance. , 2004, Journal of molecular biology.
[6] David Baker,et al. Protein-protein docking with backbone flexibility. , 2007, Journal of molecular biology.
[7] Ruth Nussinov,et al. Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies , 2005, Physical biology.
[8] Dima Kozakov,et al. Convergence and combination of methods in protein-protein docking. , 2009, Current opinion in structural biology.
[9] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[10] Zhiping Weng,et al. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking , 2005, Bioinform..
[11] Amarda Shehu,et al. An Evolutionary conservation-Based Method for Refining and Reranking protein Complex Structures , 2012, J. Bioinform. Comput. Biol..
[12] F. Cohen,et al. An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.
[13] Ruth Nussinov,et al. Geometry‐based flexible and symmetric protein docking , 2005, Proteins.
[14] Yifeng D. Yang,et al. Multi‐LZerD: Multiple protein docking for asymmetric complexes , 2012, Proteins.
[15] Amarda Shehu,et al. Guiding protein docking with Geometric and Evolutionary Information , 2012, J. Bioinform. Comput. Biol..
[16] L. T. Ten Eyck,et al. Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.
[17] Trilce Estrada,et al. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy , 2011, J. Chem. Inf. Model..
[18] D. J. Price,et al. Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.
[19] Sandor Vajda,et al. Protein-protein association kinetics and protein docking. , 2002, Current Opinion in Structural Biology.