Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking (Q37050108)

17 August 2017

Exploring the potential of protein-based pharmacophore models in ligand pose prediction and ranking (English)

1 reference

17 August 2017

Bingjie Hu

1 reference

PMC publication ID

3725268

17 August 2017

Markus A Lill

series ordinal

1 reference

17 August 2017

13 May 2013

1 reference

Journal of Chemical Information and Modeling

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

1 reference

17 August 2017

1179-1190

1 reference

Protein pharmacophore selection using hydration-site analysis

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Targets looking for drugs: a multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Hot-spots-guided receptor-based pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

The PDBbind database: methodologies and updates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Comparing protein-ligand docking programs is difficult.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Further development and validation of empirical scoring functions for structure-based binding affinity prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Automated pharmacophore identification for large chemical data sets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Automatic identification and representation of protein binding sites for molecular docking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

A geometric approach to macromolecule-ligand interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

The computer program LUDI: a new method for the de novo design of enzyme inhibitors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Identification of common functional configurations among molecules

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Comparative assessment of scoring functions on a diverse test set.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

A comparative study on the application of hierarchical-agglomerative clustering approaches to organize outputs of reiterated docking runs

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Flexible docking using Tabu search and an empirical estimate of binding affinity.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3725268

Grid-derived structure-based 3D pharmacophores and their performance compared to docking

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23621564

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CI400143R

1 reference

17 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3725268

17 August 2017

PubMed publication ID

23621564

1 reference

PMC publication ID

3725268