4.6 Article

I. Dissociation free energies of drug-receptor systems via non-equilibrium alchemical simulations: a theoretical framework

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 Feasibility of an Efficient Drug Design Method with High-Performance Computers

Takefumi Yamashita et al.

CHEMICAL & PHARMACEUTICAL BULLETIN (2015)

Article Chemistry, Physical

Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

Piero Procacci

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

Robert B. Sandberg et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Enhanced Ligand Sampling for Relative Protein-Ligand Binding Free Energy Calculations

Joseph W. Kaus et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2015)

Article Chemistry, Physical

Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange Simulations

Piero Procacci et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Fast Switching Alchemical Transformations in Molecular Dynamics Simulations

Piero Procacci et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Practical Aspects of Free-Energy Calculations: A Review

Niels Hansen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Review Biochemistry & Molecular Biology

Virtual Screening Strategies in Drug Discovery: A Critical Review

A. Lavecchia et al.

CURRENT MEDICINAL CHEMISTRY (2013)

Article Chemistry, Physical

Multiple Bennett acceptance ratio made easy for replica exchange simulations

Piero Procacci

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

James C. Gumbart et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Medicinal

Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor

Jared N. Cumming et al.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2012)

Article Chemistry, Physical

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

Vytautas Gapsys et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Chemistry, Multidisciplinary

Linear-Scaling Soft-Core Scheme for Alchemical Free Energy Calculations

Floris P. Buelens et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2012)

Article Biotechnology & Applied Microbiology

Diagnosing the decline in pharmaceutical R&D efficiency

Jack W. Scannell et al.

NATURE REVIEWS DRUG DISCOVERY (2012)

Article Biochemistry & Molecular Biology

Alchemical free energy methods for drug discovery: progress and challenges

John D. Chodera et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Advances in all atom sampling methods for modeling protein-ligand binding affinities

Emilio Gallicchio et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Molecular motions in drug design: the coming age of the metadynamics method

Xevi Biarnes et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2011)

Article Chemistry, Physical

Optimal Weights in Serial Generalized-Ensemble Simulations

Riccardo Chelli

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein Ligand Binding Affinities

Emilio Gallicchio et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

A Note on the Standard State's Binding Free Energy

Ignacio J. General

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Physical

Good Practices in Free-Energy Calculations

Andrew Pohorille et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Physical

Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors

Jeremy Fidelak et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2010)

Article Chemistry, Multidisciplinary

Water in Cavity-Ligand Recognition

Riccardo Baron et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Chemistry, Multidisciplinary

Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors

Francesco Colizzi et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Review Chemistry, Multidisciplinary

Theory of Free Energy and Entropy in Noncovalent Binding

Huan-Xiang Zhou et al.

CHEMICAL REVIEWS (2009)

Article Chemistry, Multidisciplinary

Accuracy and Convergence of Free Energy Differences Calculated from Nonequilibrium Switching Processes

Maik Goette et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Review Chemistry, Physical

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

Yuqing Deng et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Article Biotechnology & Applied Microbiology

Lessons from 60 years of pharmaceutical innovation

Bernard Munos

NATURE REVIEWS DRUG DISCOVERY (2009)

Article Physics, Fluids & Plasmas

Massively parallel computation of absolute binding free energy with well-equilibrated states

Hideaki Fujitani et al.

PHYSICAL REVIEW E (2009)

Article Chemistry, Physical

Perspective on free-energy perturbation calculations for chemical equilibria

William L. Jorgensen et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Physics, Multidisciplinary

Length of time's arrow

Edward H. Feng et al.

PHYSICAL REVIEW LETTERS (2008)

Article Chemistry, Physical

Crooks equation for steered molecular dynamics using a Nose-Hoover thermostat

Piero Procacci et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Article Chemistry, Physical

Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

Guha Jayachandran et al.

JOURNAL OF CHEMICAL PHYSICS (2006)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Chemistry, Physical

Direct calculation of the binding free energies of FKBP ligands

H Fujitani et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Article Multidisciplinary Sciences

Calculation of absolute protein-ligand binding free energy from computer simulations

HJ Woo et al.

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

Article Physics, Fluids & Plasmas

Adaptive integration method for Monte Carlo simulations

M Fasnacht et al.

PHYSICAL REVIEW E (2004)

Article Chemistry, Physical

Calculating potentials of mean force from steered molecular dynamics simulations

S Park et al.

JOURNAL OF CHEMICAL PHYSICS (2004)

Article Biophysics

On the theory of noncovalent binding

M Mihailescu et al.

BIOPHYSICAL JOURNAL (2004)

Article Multidisciplinary Sciences

Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements

J Gore et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Physics, Multidisciplinary

Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods

MR Shirts et al.

PHYSICAL REVIEW LETTERS (2003)

Article Chemistry, Physical

Absolute binding free energies: A quantitative approach for their calculation

S Boresch et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2003)

Article Multidisciplinary Sciences

Escaping free-energy minima

A Laio et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Multidisciplinary Sciences

On the calculation of absolute macromolecular binding free energies

HB Luo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Chemistry, Physical

Fast-growth thermodynamic integration: Error and efficiency analysis

G Hummer

JOURNAL OF CHEMICAL PHYSICS (2001)