4.8 Article

Adaptively Iterative Multiscale Switching Simulation Strategy and Applications to Protein Folding and Structure Prediction

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。
Article Chemistry, Physical

Arbitrary Resolution with Two Bead Types Coarse-Grained Strategy and Applications to Protein Recognition

Qinglu Zhong et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

Review Physics, Atomic, Molecular & Chemical

Advances in Enhanced Sampling Molecular Dynamics Simulations for Biomolecules

An-hui Wang et al.

CHINESE JOURNAL OF CHEMICAL PHYSICS (2019)

Review Biochemistry & Molecular Biology

Critical assessment of methods of protein structure prediction (CASP)-Round XIII

Andriy Kryshtafovych et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)

Article Chemistry, Physical

Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations

Xiangda Peng et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Chemistry, Physical

Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly

Aleksandra E. Dawid et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Biochemical Research Methods

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)

Article Biochemical Research Methods

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang et al.

NATURE METHODS (2017)

Article Chemistry, Physical

HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations

Xiaorong Liu et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)

Article Chemistry, Physical

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

Jie Hu et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2017)

Article Computer Science, Information Systems

DBSCAN Revisited, Revisited: Why and How You Should (Still) Use DBSCAN

Erich Schubert et al.

ACM TRANSACTIONS ON DATABASE SYSTEMS (2017)

Article Physics, Multidisciplinary

Smoothing potential energy surface of proteins by hybrid coarse grained approach

Yukun Lu et al.

CHINESE PHYSICS B (2017)

Article Chemistry, Multidisciplinary

Multiscale Enhanced Sampling of Intrinsically Disordered Protein Conformations

Kuo Hao Lee et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2016)

Article Chemistry, Physical

Multiscale enhanced sampling for protein systems: An extension via adiabatic separation

Kei Moritsugu et al.

CHEMICAL PHYSICS LETTERS (2016)

Review Chemistry, Multidisciplinary

Coarse-Grained Protein Models and Their Applications

Sebastian Kmiecik et al.

CHEMICAL REVIEWS (2016)

Article Chemistry, Physical

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

S. Doerr et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Review Biochemistry & Molecular Biology

Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics

Urmi Doshi et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)

Article Chemistry, Multidisciplinary

Accelerated molecular dynamics simulations of protein folding

Yinglong Miao et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)

Article Chemistry, Physical

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

Tsjerk A. Wassenaar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Multidisciplinary

Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics

Fan Jiang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)

Article Biochemistry & Molecular Biology

To milliseconds and beyond: challenges in the simulation of protein folding

Thomas J. Lane et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Chemistry, Physical

Consensus for the Fip35 folding mechanism?

Ganna Berezovska et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Perspective: Coarse-grained models for biomolecular systems

W. G. Noid

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

Parimal Kar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

Christian R. Schwantes et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations

Tsjerk A. Wassenaar et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2013)

Article Chemistry, Physical

The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics

Sergei V. Krivov

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Chemistry, Physical

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Andrzej J. Rzepiela et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Article Multidisciplinary Sciences

How Fast-Folding Proteins Fold

Kresten Lindorff-Larsen et al.

SCIENCE (2011)

Article Biochemical Research Methods

How significant is a protein structure similarity with TM-score=0.5?

Jinrui Xu et al.

BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

Atomic-Level Characterization of the Structural Dynamics of Proteins

David E. Shaw et al.

SCIENCE (2010)

Article Chemistry, Physical

Generic coarse-grained model for protein folding and aggregation

Tristan Bereau et al.

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

W. G. Noid et al.

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Multidisciplinary

Fast procedure for reconstruction of full-atom protein models from reduced representations

Piotr Rotkiewicz et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Biochemical Research Methods

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

Qiang Wang et al.

NATURE PROTOCOLS (2008)

Article Biochemistry & Molecular Biology

The Trp-cage: optimizing the stability of a globular miniprotein

Bipasha Barua et al.

PROTEIN ENGINEERING DESIGN & SELECTION (2008)

Article Biochemistry & Molecular Biology

A coarse-grained protein force field for folding and structure prediction

Julien Maupetit et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Multiscale modeling of biomolecular systems: in serial and in parallel

Gary S. Ayton et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Peptide register shifting within the MHC groove: theory becomes reality

AJ Bankovich et al.

MOLECULAR IMMUNOLOGY (2004)

Article Biochemistry & Molecular Biology

Scoring function for automated assessment of protein structure template quality

Y Zhang et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)