(Q36520871)

14 August 2017

1 reference

title

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design (English)

1 reference

14 August 2017

3

J Andrew McCammon

1 reference

14 August 2017

William Sinko

1

1 reference

14 August 2017

Steffen Lindert

series ordinal

2

1 reference

14 August 2017

language of work or name

1 reference

1 January 2013

1 reference

Chemical Biology and Drug Design

14 August 2017

1 reference

14 August 2017

81

1 reference

14 August 2017

1

1 reference

14 August 2017

41-49

1 reference

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Rosetta Ligand docking with flexible XML protocols

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

How fast-folding proteins fold

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

How does a drug molecule find its target binding site?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Predictive power of molecular dynamics receptor structures in virtual screening

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Pharmacogenomics: a systems approach

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

GPU-accelerated molecular modeling coming of age

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Computer-aided identification of Trypanosoma brucei uridine diphosphate galactose 4'-epimerase inhibitors: toward the development of novel therapies for African sleeping sickness

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Crystal Structures of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-methyl-1 H -imidazole: Ligand-Induced Structural Response through α-Helical Repositioning ,

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

DOCK 6: combining techniques to model RNA-small molecule complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Virtual screening strategies in drug discovery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Accelerating molecular modeling applications with graphics processors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

On the application of accelerated molecular dynamics to liquid water simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Structural basis for ligand promiscuity in cytochrome P450 3A4.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Application of a Theory of Enzyme Specificity to Protein Synthesis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Novel bifunctional quinolonyl diketo acid derivatives as HIV-1 integrase inhibitors: design, synthesis, biological activities, and mechanism of action

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Novel procedure for modeling ligand/receptor induced fit effects.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Flexible docking in solution using metadynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Docking and scoring in virtual screening for drug discovery: methods and applications

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Discovery of a novel binding trench in HIV integrase.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Escaping free-energy minima

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Free energy simulations come of age: protein-ligand recognition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Folding funnels and binding mechanisms

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

A geometric approach to macromolecule-ligand interactions

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Conformational selection in G-proteins: lessons from Ras and Rho.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Blind docking of pharmaceutically relevant compounds using RosettaLigand

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Soft docking and multiple receptor conformations in virtual screening

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

"Soft docking": matching of molecular surface cubes

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Exploring complex protein-ligand recognition mechanisms with coarse metadynamics

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

RosettaLigand docking with full ligand and receptor flexibility.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

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

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Ligand docking to proteins with discrete side-chain flexibility.

21 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3540989

Anton, a special-purpose machine for molecular dynamics simulation

21 September 2018

1 reference

https://api.crossref.org/works/10.1111%2FCBDD.12051

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FCBDD.12051

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FCBDD.12051

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FCBDD.12051

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FCBDD.12051

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/10.1111%2FCBDD.12051

A statistical analysis of the precision of reweighting-based simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23253130

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Use of an induced fit receptor structure in virtual screening

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23253130

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

New horizons in chemical space

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23253130

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1111/CBDD.12051

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

23253130

1 reference