(Q47374327)

http://europepmc.org/abstract/MED/29165360

15 January 2018

3 references

20 June 2019

19 September 2019

12 August 2020

Dynamic Docking: A Paradigm Shift in Computational Drug Discovery (English)

1 reference

http://europepmc.org/abstract/MED/29165360

15 January 2018

main subject

biomedical investigative technique

1 reference

19 September 2019

1 reference

12 August 2020

1 reference

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Matteo Masetti

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

author name string

Martina Bertazzo

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Maurizio Recanatini

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

Andrea Cavalli

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

language of work or name

English

0 references

publication date

22 November 2017

4 references

http://europepmc.org/abstract/MED/29165360

15 January 2018

20 June 2019

19 September 2019

12 August 2020

4 references

20 June 2019

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

12 August 2020

22

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution

10 June 2020

copyright license

3 references

20 June 2019

19 September 2019

12 August 2020

0 references

The many roles of computation in drug discovery

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Role of Molecular Dynamics and Related Methods in Drug Discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein flexibility and drug design: how to hit a moving target.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The drug-target residence time model: a 10-year retrospective

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

To milliseconds and beyond: challenges in the simulation of protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A geometric approach to macromolecule-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Exploring the role of receptor flexibility in structure-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

21 January 2018

Protein-ligand docking.

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein Flexibility in Drug Discovery: From Theory to Computation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Molecular docking and structure-based drug design strategies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Variability in docking success rates due to dataset preparation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The Energy Landscapes and Motions of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Recipes for the selection of experimental protein conformations for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Systematic exploitation of multiple receptor conformations for virtual ligand screening

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Classification of current scoring functions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Receptor-ligand molecular docking

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A computational study of the binding of propidium to the peripheral anionic site of human acetylcholinesterase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Molecular dynamics analysis to evaluate docking pose prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Combining docking and molecular dynamic simulations in drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Implicit solvent methods for free energy estimation.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Exploring complex protein-ligand recognition mechanisms with coarse metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Single-molecule pulling simulations can discern active from inactive enzyme inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A steered molecular dynamics mediated hit discovery for histone deacetylases.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Dynamic undocking and the quasi-bound state as tools for drug discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Computational approaches for fragment-based and de novo design

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Developing a dynamic pharmacophore model for HIV-1 integrase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein flexibility in docking and surface mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Molecular simulations with solvent competition quantify water displaceability and provide accurate interaction maps of protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Computational fragment-based binding site identification by ligand competitive saturation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Full protein flexibility is essential for proper hot-spot mapping.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Mapping Cholesterol Interaction Sites on Serotonin Transporter through Coarse-Grained Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Escaping free-energy minima

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Flexible docking in solution using metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Funnel metadynamics as accurate binding free-energy method

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

A bias-exchange approach to protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Electrostatic funneling of substrate in mitochondrial inner membrane carriers

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

How does a drug molecule find its target binding site?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Pathway and mechanism of drug binding to G-protein-coupled receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Structure and dynamics of the M3 muscarinic acetylcholine receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Insights from Fragment Hit Binding Assays by Molecular Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Everything you wanted to know about Markov State Models but were afraid to ask

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Markov state models of biomolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Multiscale Simulation of Receptor-Drug Association Kinetics: Application to Neuraminidase Inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Molecular recognition and ligand association

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

CHARMM: the biomolecular simulation program

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Scalable molecular dynamics with NAMD

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Calculation of relative free energy via indirect pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Exploring the recognition pathway at the human A2A adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Replica-exchange molecular dynamics simulation of small peptide in water and in ethanol

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

The role of water in host-guest interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Collecting and assessing human lactate dehydrogenase-A conformations for structure-based virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FMOLECULES22112029

Probing the alpha-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis

21 January 2018

1 reference

12 December 2020

Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations

1 reference

12 December 2020

Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials

1 reference

12 December 2020

Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design

1 reference

12 December 2020

A Note on the Standard State's Binding Free Energy

1 reference

12 December 2020

10.3390/MOLECULES22112029

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29165360%20AND%20SRC:MED&resulttype=core&format=json

10 June 2020

1 reference