(Q36098710)

12 August 2017

Docking and scoring with ICM: the benchmarking results and strategies for improvement (English)

1 reference

12 August 2017

3

Ruben Abagyan

0 references

author name string

Marco A C Neves

series ordinal

1

1 reference

PMC publication ID

3398187

12 August 2017

Maxim Totrov

series ordinal

2

1 reference

12 August 2017

9 May 2012

1 reference

Journal of Computer - Aided Molecular Design

12 August 2017

1 reference

12 August 2017

26

1 reference

12 August 2017

6

1 reference

12 August 2017

675-686

1 reference

Pocketome: an encyclopedia of small-molecule binding sites in 4D

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Triazole-linked reduced amide isosteres: an approach for the fragment-based drug discovery of anti-Alzheimer's BACE1 inhibitors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

FRED pose prediction and virtual screening accuracy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

The RCSB Protein Data Bank: redesigned web site and web services

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

n-->pi* interactions in proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Molecular recognition and drug-lead identification: what can molecular simulations tell us?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Structure-based drug design strategies in medicinal chemistry

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Discovery of potent thermolysin inhibitors using structure based virtual screening and binding assays

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Structure-based drug design: docking and scoring

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Benchmarking sets for molecular docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Molecular mechanism of citalopram and cocaine interactions with neurotransmitter transporters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Nuclear hormone receptor targeted virtual screening

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

In silico discovery of novel retinoic acid receptor agonist structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Prediction of the binding energy for small molecules, peptides and proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Flexible protein-ligand docking by global energy optimization in internal coordinates.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Chromene-3-carboxamide derivatives discovered from virtual screening as potent inhibitors of the tumour maker, AKR1B10.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Empirical scoring functions for advanced protein-ligand docking with PLANTS.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

RosettaLigand docking with full ligand and receptor flexibility.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Diverse, high-quality test set for the validation of protein-ligand docking performance.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Virtual screening against metalloenzymes for inhibitors and substrates

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Docking and scoring of metallo-beta-lactamases inhibitors

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

Molecular model of the neural dopamine transporter

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3398187

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

23 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-012-9547-0

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-012-9547-0

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-012-9547-0

pKa based protonation states and microspecies for protein–ligand docking

21 January 2018

1 reference

12 December 2020

Ligand-protein docking with water molecules

1 reference

12 December 2020

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions

1 reference

12 December 2020

Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery

1 reference

12 December 2020

From selective substrate analogue factor Xa inhibitors to dual inhibitors of thrombin and factor Xa. Part 3

1 reference

12 December 2020

Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand

1 reference

12 December 2020

10.1007/S10822-012-9547-0

Identifiers

DOI

1 reference

12 August 2017

journals/jcamd/NevesTA12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3398187

12 August 2017

PubMed publication ID

22569591

1 reference

PMC publication ID

3398187