4.7 Article

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

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

Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

Haiyang Zhang et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Review Biophysics

Biomolecular Simulation: A Computational Microscope for Molecular Biology

Ron O. Dror et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 41 (2012)

Article Chemistry, Multidisciplinary

Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

Xavier Periole et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Chemistry, Medicinal

Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method

Nadine Homeyer et al.

MOLECULAR INFORMATICS (2012)

Review Chemistry, Physical

Coarse-grained molecular models of water: a review

Kevin R. Hadley et al.

MOLECULAR SIMULATION (2012)

Article Physics, Mathematical

Physical Modeling of Aqueous Solvation

Christopher J. Fennell et al.

JOURNAL OF STATISTICAL PHYSICS (2011)

Article Chemistry, Physical

Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes

Hiraku Oshima et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)

Article Biochemical Research Methods

Are Scoring Functions in Protein-Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

Panagiotis L. Kastritis et al.

JOURNAL OF PROTEOME RESEARCH (2010)

Article Chemistry, Physical

The influence of micelle formation on the stability of colloid surfactant mixtures

Rene Pool et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)

Article Biochemistry & Molecular Biology

Present and future challenges and limitations in protein-protein docking

Carles Pons et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Blind predictions of protein interfaces by docking calculations in CAPRI

Marc F. Lensink et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Review Biochemical Research Methods

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

Nurcan Tuncbag et al.

BRIEFINGS IN BIOINFORMATICS (2009)

Review Biochemical Research Methods

Progress and challenges in predicting protein-protein interaction sites

Lakes Ezkurdia et al.

BRIEFINGS IN BIOINFORMATICS (2009)

Article Chemistry, Physical

The MARTINI coarse-grained force field: Extension to proteins

Luca Monticelli et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Physical

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Berk Hess et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Biochemistry & Molecular Biology

Molecular dynamics-solvated interaction energy studies of protein-protein interactions:: The MP1-p14 scaffolding complex

Qizhi Cui et al.

JOURNAL OF MOLECULAR BIOLOGY (2008)

Article Multidisciplinary Sciences

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association

Chia-en A. Chang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Chemistry, Physical

The MARTINI force field: Coarse grained model for biomolecular simulations

Siewert J. Marrink et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Biochemical Research Methods

Protein-protein interaction hotspots carved into sequences

Yanay Ofran et al.

PLOS COMPUTATIONAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

T cell receptor binding transition states and recognition of peptide/MHC

Rebecca L. Davis-Harrison et al.

BIOCHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Prediction of structures of multidomain proteins from structures of the individual domains

Andrew M. Wollacott et al.

PROTEIN SCIENCE (2007)

Article Chemistry, Physical

A comparison of methods to compute the potential of mean force

Daniel Trzesniak et al.

CHEMPHYSCHEM (2007)

Article Chemistry, Physical

Dynamic distance disorder in proteins is caused by trapping

Guobin Luo et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2006)

Article Biochemistry & Molecular Biology

Flexibility and conformational entropy in protein-protein binding

R Grünberg et al.

STRUCTURE (2006)

Review Multidisciplinary Sciences

Progress on modeling of protein structures and interactions

O Schueler-Furman et al.

SCIENCE (2005)

Article Multidisciplinary Sciences

Conservation and relative importance of residues across protein-protein interfaces

M Guharoy et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Crystal structure of the p14/MP1 scaffolding complex flow a twin couple attaches mitogen-activated protein kinase signaling to late endosomes

R Kurzbauer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Article Biochemistry & Molecular Biology

How reliable are experimental protein-protein interaction data?

E Sprinzak et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Multidisciplinary Sciences

Two-step binding mechanism for T-cell receptor recognition of peptide-MHC

LC Wu et al.

NATURE (2002)