Related references
Note: Only part of the references are listed.Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field
Michal Jamroz et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Smoothing of the GB1 Hairpin Folding Landscape by Interfacial Confinement
Apratim Bhattacharya et al.
BIOPHYSICAL JOURNAL (2012)
Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method
Sidhartha Chaudhury et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
From Coarse-Grained to Atomic-Level Characterization of Protein Dynamics: Transition State for the Folding of B Domain of Protein A
Sebastian Kmiecik et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Optimization of protein models
Dominik Gront et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
Stefano Piana et al.
BIOPHYSICAL JOURNAL (2011)
Why the OPLS-AA Force Field Cannot Produce the β-Hairpin Structure of H1 Peptide in Solution When Comparing with the GROMOS 43A1 Force Field?
Zanxia Cao et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2011)
Velocity scaling for optimizing replica exchange molecular dynamics
Maksim Kouza et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Structure change of β-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study
Qiang Shao et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation-Condensation to Framework Mechanism
Sebastian Kmiecik et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models
Dietmar Paschek et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Coarse-grained force field: general folding theory
Adam Liwo et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
Robert B. Best et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Mechanism of Formation of the C-Terminal β-Hairpin of the B3 Domain of the Immunoglobulin-Binding Protein G from Streptococcus. IV. Implication for the Mechanism of Folding of the Parent Protein
Agnieszka Lewandowska et al.
BIOPOLYMERS (2010)
A Comparative Study of Two Different Force Fields on Structural and Thermodynamics Character of H1 Peptide via Molecular Dynamics Simulations
Zanxia Cao et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2010)
Balance between a and β Structures in Ab Initio Protein Folding
Robert B. Best et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Protein mechanical unfolding: Importance of non-native interactions
Maksim Kouza et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
CHARMM: The Biomolecular Simulation Program
B. R. Brooks et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation
Agnieszka Skwierawska et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure
Agnieszka Skwierawska et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)
Utility library for structural bioinformatics
Dominik Gront et al.
BIOINFORMATICS (2008)
Folding pathway of the B1 domain of protein G explored by multiscale modeling
Sebastian Kmiecik et al.
BIOPHYSICAL JOURNAL (2008)
Investigating the mechanism of peptide aggregation: Insights from mixed Monte Carlo-Molecular dynamics simulations
Massimiliano Meli et al.
BIOPHYSICAL JOURNAL (2008)
New force replica exchange method and protein folding pathways probed by force-clamp technique
Maksim Kouza et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Berk Hess et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Peptide Folding Using Multiscale Coarse-Grained Models
Ian F. Thorpe et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin
Angel E. Garcia et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Computing the stability diagram Trp-cage miniprotein of the
Dietmar Paschek et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation
Eunae Kim et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Characterization of protein-folding pathways by reduced-space modeling
Sebastian Kmiecik et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
Dominik Gront et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
Sebastian Kmiecik et al.
BMC STRUCTURAL BIOLOGY (2007)
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir
Adrian E. Roitberg et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Efficient scheme for optimization of parallel tempering Monte Carlo method
Dominik Gront et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2007)
Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations
Chia-En A. Chang et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2007)
Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir
Asim Okur et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Force field influences in β-hairpin folding simulations
Thu Zar Lwin et al.
PROTEIN SCIENCE (2006)
Protein folding simulations: combining coarse-grained models and all-atom molecular dynamics
Giorgio Colombo et al.
THEORETICAL CHEMISTRY ACCOUNTS (2006)
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
Eugene Shakhnovich
CHEMICAL REVIEWS (2006)
BioShell - a package of tools for structural biology computations
D Gront et al.
BIOINFORMATICS (2006)
GROMACS: Fast, flexible, and free
D Van der Spoel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
Free energy landscape and folding mechanism of a β-hairpin in explicit water:: A replica exchange molecular dynamics study
PH Nguyen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Reproducible polypeptide folding and structure prediction using molecular dynamics simulations
MM Seibert et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Theoretical model of prion propagation: A misfolded protein induces misfolding
E Malolepsza et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Coarse-grained models for proteins
V Tozzini
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models
A Kolinski et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structures
GMS De Mori et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Understanding the key factors that control the rate of β-hairpin folding
DG Du et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
A graph-theory algorithm for rapid protein side-chain prediction
AA Canutescu et al.
PROTEIN SCIENCE (2003)
A minimal physically realistic protein-like lattice model: Designing an energy landscape that ensures all-or-none folding to a unique native state
P Pokarowski et al.
BIOPHYSICAL JOURNAL (2003)
The free energy landscape for β hairpin folding in explicit water
RH Zhou et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics
D Gront et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Share Paper
