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。Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
Anna Antoniak et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2021)
Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2
Yuanpeng Janet Huang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021)
Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
Arup Mondal et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2021)
ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons
Emilia A. Lubecka et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2021)
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
Adam Liwo et al.
JOURNAL OF CHEMICAL PHYSICS (2019)
Introduction of a Bounded Penalty Function in Contact-Assisted Simulations of Protein Structures to Omit False Restraints
Emilia A. Lubecka et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2019)
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications
Nidhi Singh et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)
De novo protein design by citizen scientists
Brian Koepnick et al.
NATURE (2019)
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
Emilia A. Lubecka et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2019)
Protein structure prediction assisted with sparse NMR data in CASP13
Davide Sala et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains
Adam K. Sieradzan et al.
JOURNAL OF CHEMICAL PHYSICS (2017)
Ergodicity and Model Quality in Template-Restrained Canonical and Temperature/Hamiltonian Replica Exchange Coarse-Grained Molecular Dynamics Simulations of Proteins
Agnieszka S. Karczynska et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
Introduction of Steered Molecular Dynamics into UNRES Coarse-Grained Simulations Package
Adam K. Sieradzan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)
A community resource of experimental data for NMR/X-ray crystal structure pairs
John K. Everett et al.
PROTEIN SCIENCE (2016)
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Pawel Krupa et al.
BIOINFORMATICS (2016)
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik et al.
CHEMICAL REVIEWS (2016)
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
Shoji Takada et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Protein structure determination by conformational space annealing using NMR geometric restraints
Keehyoung Joo et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2015)
Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations
Fabian Zeller et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation
Aram Davtyan et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions
Adam Liwo et al.
JOURNAL OF MOLECULAR MODELING (2014)
Perspective on the Martini model
Siewert J. Marrink et al.
CHEMICAL SOCIETY REVIEWS (2013)
The Theory of Ultra-Coarse-Graining. 1. General Principles
James F. Dama et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
Aram Davtyan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
CABS-NMR-De Novo Tool for Rapid Global Fold Determination From Chemical Shifts, Residual Dipolar Couplings and Sparse Methyl-Methyl NOEs
Dorota Latek et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α plus β Proteins
Cezary Czaplewski et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
The MARTINI coarse-grained force field: Extension to proteins
Luca Monticelli et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Fast procedure for reconstruction of full-atom protein models from reduced representations
Piotr Rotkiewicz et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
Qiang Wang et al.
NATURE PROTOCOLS (2008)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins
Adam Liwo et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function
Franciszek Rakowski et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Optimized parallel tempering simulations of proteins
S Trebst et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Molecular dynamics with the united-residue model of polypeptide chains.: II.: Langevin and Berendsen-Bath dynamics and tests on model α-helical systems
M Khalili et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Reduced models of proteins and their applications
A Kolinski et al.
POLYMER (2004)
LGA: a method for finding 3D similarities in protein structures
A Zemla
NUCLEIC ACIDS RESEARCH (2003)
Packing helices in proteins by global optimization of a potential energy function
M Nanias et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Multiplexed-replica exchange molecular dynamics method for protein folding simulation
YM Rhee et al.
BIOPHYSICAL JOURNAL (2003)
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
H Fukunishi et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)
分享论文
