Related references
Note: Only part of the references are listed.Finding chemical drugs for genetic diseases
Hui-Yong Sun et al.
DRUG DISCOVERY TODAY (2014)
Unbinding Pathways of VEGFR2 Inhibitors Revealed by Steered Molecular Dynamics
Anna Maria Capelli et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Exploring Transition Pathway and Free-Energy Profile of Large-Scale Protein Conformational Change by Combining Normal Mode Analysis and Umbrella Sampling Molecular Dynamics
Jinan Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set
Huiyong Sun et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring
Huiyong Sun et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
Huiyong Sun et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
The Dynamic Process of β2-Adrenergic Receptor Activation
Rie Nygaard et al.
CELL (2013)
Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy
Hui-Yong Sun et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
Huiyong Sun et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches
Peichen Pan et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
James C. Gumbart et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Free energy landscape for the binding process of Huperzine A to acetylcholinesterase
Fang Bai et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435
Weiwei Xue et al.
ANTIVIRAL RESEARCH (2012)
Sequence, Structure, and Active Site Analyses of p38 MAP Kinase: Exploiting DFG-out Conformation as a Strategy to Design New Type II Leads
Preethi Badrinarayan et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase
Ying Yang et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
Tingjun Hou et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase
Jean-Francois St-Pierre et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Activation mechanism of the β2-adrenergic receptor
Ron O. Dror et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Umbrella sampling
Johannes Kaestner
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
Insights into MAPK p38α DFG flip mechanism by accelerated molecular dynamics
Federico Filomia et al.
BIOORGANIC & MEDICINAL CHEMISTRY (2010)
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
Jerome Henin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications
Peter Ripphausen et al.
JOURNAL OF MEDICINAL CHEMISTRY (2010)
Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force
Slimane Doudou et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl
Li-Jun Yang et al.
PLOS ONE (2009)
Adaptive biasing force method for scalar and vector free energy calculations
Eric Darve et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Alessandro Laio et al.
REPORTS ON PROGRESS IN PHYSICS (2008)
Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance
Tingjun Hou et al.
JOURNAL OF MEDICINAL CHEMISTRY (2007)
Rational design of inhibitors that bind to inactive kinase conformations
Y Liu et al.
NATURE CHEMICAL BIOLOGY (2006)
Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase
Tamara Frembgen-Kesner et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
Molecular dynamics: Survey of methods for simulating the activity of proteins
Stewart A. Adcock et al.
CHEMICAL REVIEWS (2006)
The Amber biomolecular simulation programs
DA Case et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)
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)
Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF
PTC Wan et al.
CELL (2004)
Development and testing of a general amber force field
JM Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
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)
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Y Duan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Issues and progress with protein kinase inhibitors for cancer treatment
J Dancey et al.
NATURE REVIEWS DRUG DISCOVERY (2003)
The protein kinase complement of the human genome
G Manning et al.
SCIENCE (2002)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Structural biology in drug design: selective protein kinase inhibitors
G Scapin
DRUG DISCOVERY TODAY (2002)
The conformational plasticity of protein kinases
M Huse et al.
CELL (2002)
Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site
C Pargellis et al.
NATURE STRUCTURAL BIOLOGY (2002)
Protein kinases - the major drug targets of the twenty-first century?
P Cohen
NATURE REVIEWS DRUG DISCOVERY (2002)
Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: Insight into structure-based ligand design
SH Huo et al.
JOURNAL OF MEDICINAL CHEMISTRY (2002)
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
JM Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)
Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations
M Souaille et al.
COMPUTER PHYSICS COMMUNICATIONS (2001)
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
PA Kollman et al.
ACCOUNTS OF CHEMICAL RESEARCH (2000)
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
B Kuhn et al.
JOURNAL OF MEDICINAL CHEMISTRY (2000)
Structural mechanism for STI-571 inhibition of Abelson tyrosine kinase
T Schindler et al.
SCIENCE (2000)
Share Paper
