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。Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2
Veronica Salmaso et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2018)
AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein-Ligand Association
Alberto Cuzzolin et al.
CHEMMEDCHEM (2018)
Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking
Claas Strecker et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)
Structure-Guided Modification of Heterocyclic Antagonists of the P2Y14 Receptor
Jinha Yu et al.
JOURNAL OF MEDICINAL CHEMISTRY (2018)
Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations
Fabian Paul et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2018)
High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble
Laura R. Ganser et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)
High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble
Laura R. Ganser et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)
Graphics processing units in bioinformatics, computational biology and systems biology
Marco S. Nobile et al.
BRIEFINGS IN BIOINFORMATICS (2017)
An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands
Noureldin Saleh et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)
The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery
Francesca Spyrakis et al.
JOURNAL OF MEDICINAL CHEMISTRY (2017)
Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example
Giuseppe Deganutti et al.
MOLECULES (2017)
Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach
Veronica Salmaso et al.
STRUCTURE (2017)
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Fabian Paul et al.
NATURE COMMUNICATIONS (2017)
Recent advances in dynamic docking for drug discovery
Marco De Vivo et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2017)
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik et al.
CHEMICAL REVIEWS (2016)
Impact of Surface Water Layers on Protein Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?
Michael Betz et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations
Alberto Cuzzolin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)
DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015
Veronica Salmaso et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2016)
Role of Molecular Dynamics and Related Methods in Drug Discovery
Marco De Vivo et al.
JOURNAL OF MEDICINAL CHEMISTRY (2016)
Picosecond to Millisecond Structural Dynamics in Human Ubiquitin
Kresten Lindorff-Larsen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Multiensemble Markov models of molecular thermodynamics and kinetics
Hao Wu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000
Giuseppe Deganutti et al.
BIOORGANIC & MEDICINAL CHEMISTRY (2015)
A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics
Quan Van Vuong et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
AceCloud: Molecular Dynamics Simulations in the Cloud
M. J. Harvey et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
Francesca Spyrakis et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)
Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
Elizabeth Yuriev et al.
JOURNAL OF MOLECULAR RECOGNITION (2015)
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
Kalli Kappel et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2015)
Exploring the recognition pathway at the human A2A adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations
Davide Sabbadin et al.
MEDCHEMCOMM (2015)
PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking
Marcus C. K. Ng et al.
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY (2015)
Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
Edina Rosta et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Molecular Mechanics
Kenno Vanommeslaeghe et al.
CURRENT PHARMACEUTICAL DESIGN (2014)
Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5
Jagdish Suresh Patel et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR-Ligand Recognition: The Human A(2A) Adenosine Receptor as a Key Study
Davide Sabbadin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR-Ligand Recognition Pathway in a Nanosecond Time Scale
Davide Sabbadin et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations
S. Doerr et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
Sergio Ruiz-Carmona et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Computational Methods in Drug Discovery
Gregory Sliwoski et al.
PHARMACOLOGICAL REVIEWS (2014)
Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study
Andrea Bortolato et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)
Prediction of Protein-Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations: Application to Kinase Systems
Hironori Kokubo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
The emerging role of cloud computing in molecular modelling
Jean-Paul Ebejer et al.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2013)
Fast Docking on Graphics Processing Units via Ray-Casting
Karen R. Khar et al.
PLOS ONE (2013)
Funnel metadynamics as accurate binding free-energy method
Vittorio Limongelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
High-throughput molecular dynamics: the powerful new tool for drug discovery
Matthew J. Harvey et al.
DRUG DISCOVERY TODAY (2012)
Variability in docking success rates due to dataset preparation
Christopher R. Corbeil et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)
Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols
David J. Osguthorpe et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Structure and dynamics of the M3 muscarinic acetylcholine receptor
Andrew C. Kruse et al.
NATURE (2012)
Molecular dynamics simulations and drug discovery
Jacob D. Durrant et al.
BMC BIOLOGY (2011)
Accelerating Molecular Docking Calculations Using Graphics Processing Units
Oliver Korb et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Ab Initio Prediction of Protein-Ligand Binding Structures by Replica-Exchange Umbrella Sampling Simulations
Hironori Kokubo et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
How Does a Drug Molecule Find Its Target Binding Site?
Yibing Shan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Pathway and mechanism of drug binding to G-protein-coupled receptors
Ron O. Dror et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Ignasi Buch 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)
Metadynamics
Alessandro Barducci et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)
From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions
Huan-Xiang Zhou
BIOPHYSICAL JOURNAL (2010)
Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic
Tanaji T. Talele et al.
CURRENT TOPICS IN MEDICINAL CHEMISTRY (2010)
Advances and Challenges in Protein-Ligand Docking
Sheng-You Huang et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2010)
Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
Gregory R. Bowman et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Software News and Update AutoDock Vina: Improving the Speed and Accuracy of Docking with a New Scoring Function, Efficient Optimization, and Multithreading
Oleg Trott et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4′-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness
Jacob D. Durrant et al.
JOURNAL OF MEDICINAL CHEMISTRY (2010)
Everything you wanted to know about Markov State Models but were afraid to ask
Vijay S. Pande et al.
METHODS (2010)
Folding and binding cascades: Dynamic landscapes and population shifts
Sandeep Kumar et al.
PROTEIN SCIENCE (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Peter Csermely et al.
TRENDS IN BIOCHEMICAL SCIENCES (2010)
Binding Estimation after Refinement, a New Automated Procedure for the Refinement and Rescoring of Docked Ligands in Virtual Screening
Giulio Rastelli et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2009)
Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
Oliver Korb et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2009)
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
M. J. Harvey et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Accelerating Molecular Dynamic Simulation on Graphics Processing Units
Mark S. Friedrichs et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Ligand Entry and Exit Pathways in the β2-Adrenergic Receptor
Ting Wang et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Ligand binding to proteins: The binding landscape model
David W. Miller et al.
PROTEIN SCIENCE (2009)
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
Nicolas Sauton et al.
BMC BIOINFORMATICS (2008)
Anton, a special-purpose machine for molecular dynamics simulation
David E. Shaw et al.
COMMUNICATIONS OF THE ACM (2008)
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
Rommie E. Amaro et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2008)
Harvesting graphics power for MD simulations
J. A. van Meel et al.
MOLECULAR SIMULATION (2008)
A temperature predictor for parallel tempering simulations
Alexandra Patriksson et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
Alessandro Barducci et al.
PHYSICAL REVIEW LETTERS (2008)
Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
Kei-ichi Okazaki et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (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)
Dynamic personalities of proteins
Katherine Henzler-Wildman et al.
NATURE (2007)
PSO@AUTODOCK:: A fast flexible molecular docking program based on swarm intelligence
Vigneshwaran Namasivayam et al.
CHEMICAL BIOLOGY & DRUG DESIGN (2007)
Computer-aided drug design: the next 20 years
John H. Van Drie
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2007)
Conformational complexity of G-protein-coupled receptors
Brian K. Kobilka et al.
TRENDS IN PHARMACOLOGICAL SCIENCES (2007)
A semiempirical free energy force field with charge-based desolvation
Ruth Huey et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
Sheng-You Huang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)
SODOCK: Swarm optimization for highly flexible protein-ligand docking
Hung-Ming Chen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
Jens Meiler et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
Richard A. Friesner et al.
JOURNAL OF MEDICINAL CHEMISTRY (2006)
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
Giovanni Bussi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Molecular dynamics: Survey of methods for simulating the activity of proteins
Stewart A. Adcock et al.
CHEMICAL REVIEWS (2006)
PSI-DOCK: Towards highly efficient and accurate flexible ligand docking
JF Pei et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
General and targeted statistical potentials for protein-ligand interactions
WTM Mooij et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)
Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method:: umbrella integration -: art. no. 144104
J Kästner et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
DrugScoreCSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
HFG Velec et al.
JOURNAL OF MEDICINAL CHEMISTRY (2005)
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
P Liu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Flexible docking in solution using metadynamics
FL Gervasio et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Discovery of a novel binding trench in HIV integrase
JR Schames et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
RA Friesner et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
TA Halgren et al.
JOURNAL OF MEDICINAL CHEMISTRY (2004)
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
D Hamelberg et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Docking and scoring in virtual screening for drug discovery: Methods and applications
DB Kitchen et al.
NATURE REVIEWS DRUG DISCOVERY (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Structure-based design of aliskiren, a novel orally effective renin inhibitor
JM Wood et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2003)
Improved protein-ligand docking using GOLD
ML Verdonk et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2003)
Implications of protein flexibility for drug discovery
SJ Teague
NATURE REVIEWS DRUG DISCOVERY (2003)
Thermodynamic contributions of the ordered water molecule in HIV-1 protease
Z Li et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
VS Pande et al.
BIOPOLYMERS (2003)
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
JH Lin et al.
BIOPOLYMERS (2003)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Principles of docking: An overview of search algorithms and a guide to scoring functions
I Halperin et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2002)
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
H Fukunishi et al.
JOURNAL OF CHEMICAL PHYSICS (2002)
Computational drug design accommodating receptor flexibility: The relaxed complex scheme
JH Lin et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
A review of protein-small molecule docking methods
RD Taylor et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2002)
EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
YP Pang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2001)
High-throughput docking for lead generation
R Abagyan et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2001)
Steered molecular dynamics and mechanical functions of proteins
B Isralewitz et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2001)
How do substrates enter and products exit the buried active site of cytochrome P450cam?: 1.: Random expulsion molecular dynamics investigation of ligand access channels and mechanisms
SK Lüdemann et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
Multidimensional replica-exchange method for free-energy calculations
Y Sugita et al.
JOURNAL OF CHEMICAL PHYSICS (2000)
Knowledge-based scoring function to predict protein-ligand interactions
H Gohlke et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
The Protein Data Bank
HM Berman et al.
NUCLEIC ACIDS RESEARCH (2000)