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。Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Agnieszka S. Karczynska et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Lipophilicity of Coarse-Grained Cholesterol Models
Franccesca Fornasier et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Improved protein structure prediction using potentials from deep learning
Andrew W. Senior et al.
NATURE (2020)
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study
Junmei Wang
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
A Review on Applications of Computational Methods in Drug Screening and Design
Xiaoqian Lin et al.
MOLECULES (2020)
Recent Open Issues in Coarse Grained Force Fields
Felipe Rodrigues Souza et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Tuning the hydrophobicity of a coarse grained model of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using the experimental octanol-water partition coefficient
Lucas M. P. Souza et al.
JOURNAL OF MOLECULAR LIQUIDS (2020)
'IT WILL CHANGE EVERYTHING': DEEPMIND'S AI MAKES GIGANTIC LEAP IN SOLVING PROTEIN STRUCTURES
Ewen Callaway
NATURE (2020)
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)
CASP13 target classification into tertiary structure prediction categories
Lisa N. Kinch et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)
Assessment of protein assembly prediction in CASP13
Dmytro Guzenko et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (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)
MIST: A simple and efficient molecular dynamics abstraction library for integrator development
Iain Bethune et al.
COMPUTER PHYSICS COMMUNICATIONS (2019)
Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
Agnieszka S. Karczynska et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)
Assessment of protein assembly prediction in CASP12
Aleix Lafita et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2018)
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core
Lukas Zimmermann et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
Agnieszka Karczynska et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2018)
SWISS-MODEL: homology modelling of protein structures and complexes
Andrew Waterhouse et al.
NUCLEIC ACIDS RESEARCH (2018)
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks
Badri Adhikari et al.
BIOINFORMATICS (2018)
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)
Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides
Philipp S. Schmalhorst et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11
Wenxuan Zhang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2016)
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Pawel Krupa et al.
BIOINFORMATICS (2016)
DeepQA: improving the estimation of single protein model quality with deep belief networks
Renzhi Cao et al.
BMC BIOINFORMATICS (2016)
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik et al.
CHEMICAL REVIEWS (2016)
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
Magdalena A. Mozolewska et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry
David W. Ritchie et al.
JOURNAL OF APPLIED CRYSTALLOGRAPHY (2016)
Protein-Protein Docking: From Interaction to Interactome
Ilya A. Vakser
BIOPHYSICAL JOURNAL (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)
WeFold: A coopetition for protein structure prediction
George A. Khoury et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2014)
Toward Optimized Potential Functions for Protein-Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field
Austin C. Stark et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation
Kresten Lindorff-Larsen et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
Daniel S. D. Larsson et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
Molecular dynamics simulations and drug discovery
Jacob D. Durrant et al.
BMC BIOLOGY (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)
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Mark S. Friedrichs et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction
Takeshi N. Sasaki et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2008)
Anton, a special-purpose machine for molecular dynamics simulation
David E. Shaw et al.
COMMUNICATIONS OF THE ACM (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)
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. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode
M Khalili et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
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)
A coarse-grained Langevin molecular dynamics approach to protein structure reproduction
TN Sasaki et al.
CHEMICAL PHYSICS LETTERS (2005)
LGA: a method for finding 3D similarities in protein structures
A Zemla
NUCLEIC ACIDS RESEARCH (2003)
Multiplexed-replica exchange molecular dynamics method for protein folding simulation
YM Rhee et al.
BIOPHYSICAL JOURNAL (2003)
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
VS Pande et al.
BIOPOLYMERS (2003)
Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
A Liwo et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
The PSIPRED protein structure prediction server
LJ McGuffin et al.
BIOINFORMATICS (2000)
分享论文
