4.6 Article

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations

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, Medicinal

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

Samuel Genheden et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Physical

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

Bill R. Miller et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Medicinal

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

Nadine Homeyer et al.

MOLECULAR INFORMATICS (2012)

Article Chemistry, Physical

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

Jimmy Heimdal et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2012)

Article Biochemistry & Molecular Biology

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

Samuel Genheden et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2012)

Article Chemistry, Medicinal

A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series

Chaya Rapp et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Multidisciplinary

Quantum Mechanical Binding Free Energy Calculation for Phosphopeptide Inhibitors of the Lck SH2 Domain

Victor M. Anisimov et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Chemistry, Physical

Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation

Michal Kolar et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2011)

Article Chemistry, Multidisciplinary

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

Samuel Genheden et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Chemistry, Physical

An MM/3D-RISM Approach for Ligand Binding Affinities

Samuel Genheden et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Multidisciplinary

Protein Flexibility and Conformational Entropy in Ligand Design Targeting the Carbohydrate Recognition Domain of Galectin-3

Carl Diehl et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Biochemistry & Molecular Biology

An improved method to predict the entropy term with the MM/PBSA approach

Jacob Kongsted et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2009)

Article Chemistry, Medicinal

MM-GB/SA rescoring of docking poses in structure-based lead optimization

Cristiano R. W. Guimaraes et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)

Article Chemistry, Physical

Accurate and efficient corrections for missing dispersion interactions in molecular Simulations

Michael R. Shirts et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Review Pharmacology & Pharmacy

The role of quantum mechanics in structure-based drug design

Kaushik Raha et al.

DRUG DISCOVERY TODAY (2007)

Article Chemistry, Physical

Generalized Born model with a simple, robust molecular volume correction

John Mongan et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Chemistry, Medicinal

Ligand affinities predicted with the MM/PBSA method:: Dependence on the simulation method and the force field

Aaron Weis et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

Review Biochemistry & Molecular Biology

Towards predictive ligand design with free-energy based computational methods?

N. Foloppe et al.

CURRENT MEDICINAL CHEMISTRY (2006)

Article Chemistry, Medicinal

Validation and use of the MM-PBSA approach for drug discovery

B Kuhn et al.

JOURNAL OF MEDICINAL CHEMISTRY (2005)

Article Physics, Multidisciplinary

Quantum mechanical free energy barrier for an enzymatic reaction

TH Rod et al.

PHYSICAL REVIEW LETTERS (2005)

Article Chemistry, Multidisciplinary

Development and testing of a general amber force field

JM Wang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Physical

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

HW Horn et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biochemistry & Molecular Biology

Exploring protein native states and large-scale conformational changes with a modified generalized born model

A Onufriev et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Molecular dynamics in the endgame of protein structure prediction

MR Lee et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Review Chemistry, Multidisciplinary

Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models

PA Kollman et al.

ACCOUNTS OF CHEMICAL RESEARCH (2000)