Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta
Authors
Keywords
-
Journal
PLoS One
Volume 10, Issue 6, Pages e0125941
Publisher
Public Library of Science (PLoS)
Online
2015-06-09
DOI
10.1371/journal.pone.0125941
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A General Computational Approach for Repeat Protein Design
- (2015) Fabio Parmeggiani et al. JOURNAL OF MOLECULAR BIOLOGY
- Protein folding, structure prediction and design
- (2014) David Baker BIOCHEMICAL SOCIETY TRANSACTIONS
- Search strategies and evaluation in protein–protein docking: principles, advances and challenges
- (2014) Sheng-You Huang DRUG DISCOVERY TODAY
- Protein–Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials
- (2014) Manuel P. Luitz et al. Journal of Chemical Information and Modeling
- Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins
- (2013) Katja Ostermeir et al. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
- An accurate binding interaction model in de novo computational protein design of interactions: If you build it, they will bind
- (2013) Nir London et al. JOURNAL OF STRUCTURAL BIOLOGY
- Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock
- (2013) Zhe Zhang et al. PLoS One
- Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble
- (2012) Michael Deighan et al. Journal of Chemical Theory and Computation
- How Many Protein-Protein Interactions Types Exist in Nature?
- (2012) Leonardo Garma et al. PLoS One
- Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
- (2011) Sidhartha Chaudhury et al. PLoS One
- A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions
- (2011) Maxim V. Shapovalov et al. STRUCTURE
- Metadynamics
- (2011) Alessandro Barducci et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Enhanced Sampling in the Well-Tempered Ensemble
- (2010) M. Bonomi et al. PHYSICAL REVIEW LETTERS
- Docking and scoring protein interactions: CAPRI 2009
- (2010) Marc F. Lensink et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein-protein docking benchmark version 4.0
- (2010) Howook Hwang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Convergence and combination of methods in protein–protein docking
- (2009) Sandor Vajda et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Hamiltonian replica exchange molecular dynamics using soft-core interactions
- (2008) Jozef Hritz et al. JOURNAL OF CHEMICAL PHYSICS
- Minimizing and Learning Energy Functions for Side-Chain Prediction
- (2008) Chen Yanover et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
- Estimating the size of the human interactome
- (2008) M. P. H. Stumpf et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Protein-protein docking benchmark version 3.0
- (2008) Howook Hwang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
- (2008) Alessandro Laio et al. REPORTS ON PROGRESS IN PHYSICS
- Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels
- (2008) Nir London et al. STRUCTURE
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started