eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models (Q39531365)

12 September 2017

eFindSite: Enhanced Fingerprint-Based Virtual Screening Against Predicted Ligand Binding Sites in Protein Models (English)

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12 September 2017

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2

Michal Brylinski

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12 September 2017

Wei P Feinstein

1

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12 September 2017

12 February 2014

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12 September 2017

Molecular Informatics

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12 September 2017

33

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12 September 2017

135-150

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12 September 2017

2

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On evaluating molecular-docking methods for pose prediction and enrichment factors

12 September 2017

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https://api.crossref.org/works/10.1002%2FMINF.201300143

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Improved protein-ligand docking using GOLD

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Identification of a sub-micromolar, non-peptide inhibitor of β-secretase with low neural cytotoxicity through in silico screening.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

3-oxoacyl-ACP reductase from Schistosoma japonicum: integrated in silico-in vitro strategy for discovering antischistosomal lead compounds

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Discovery of the inhibitory effect of a phosphatidylinositol derivative on P-glycoprotein by virtual screening followed by in vitro cellular studies

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Assessing scoring functions for protein-ligand interactions.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Systems biology and new technologies enable predictive and preventative medicine.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Twilight zone of protein sequence alignments

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Data growth and its impact on the SCOP database: new developments

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Analysis of catalytic residues in enzyme active sites.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Cheminformatics at the interface of medicinal chemistry and proteomics

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Structure-based systems biology for analyzing off-target binding

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

What does systems biology mean for drug development?

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Protein structure prediction: when is it useful?

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

eFindSite: improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Supersites within superfolds. Binding site similarity in the absence of homology.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

FINDSITE: a threading-based approach to ligand homology modeling

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

eThread: a highly optimized machine learning-based approach to meta-threading and the modeling of protein tertiary structures

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

KEGG: Kyoto Encyclopedia of Genes and Genomes

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

ZINC--a free database of commercially available compounds for virtual screening

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

PISCES: a protein sequence culling server

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Scoring function for automated assessment of protein structure template quality

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Benchmarking sets for molecular docking

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Comparative protein modelling by satisfaction of spatial restraints

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

A scoring function for docking ligands to low-resolution protein structures.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Approaches to Measure Chemical Similarity– a Review

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Reoptimization of MDL keys for use in drug discovery

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Design and evaluation of a molecular fingerprint involving the transformation of property descriptor values into a binary classification scheme.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

Chemical Similarity Searching

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

The Blue Obelisk-interoperability in chemical informatics

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

BindingDB: a web-accessible molecular recognition database

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

DrugBank: a comprehensive resource for in silico drug discovery and exploration

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

21 January 2018

The Protein Data Bank

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https://api.crossref.org/works/10.1002%2FMINF.201300143

National Cancer Institute Drug Information System 3D database.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

ChEMBL: a large-scale bioactivity database for drug discovery

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Comparison of the NCI open database with seven large chemical structural databases.

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

The complete genome sequence of Escherichia coli K-12

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

TASSER-Lite: an automated tool for protein comparative modeling

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Combination of fingerprint-based similarity coefficients using data fusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

Analysis of data fusion methods in virtual screening: similarity and group fusion

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

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

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Virtual screening data fusion using both structure- and ligand-based methods

21 January 2018

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https://api.crossref.org/works/10.1002%2FMINF.201300143

Protein-ligand docking against non-native protein conformers

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

The ABC transporter structure and mechanism: perspectives on recent research.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

Characterization of lptA and lptB, two essential genes implicated in lipopolysaccharide transport to the outer membrane of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

Functional analysis of the protein machinery required for transport of lipopolysaccharide to the outer membrane of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FMINF.201300143

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

21 January 2018

1 reference

COCI

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201300143

Evaluations of molecular docking programs for virtual screening

8 April 2023

1 reference

COCI

https://opencitations.net/index/coci/api/v1/references/10.1002/MINF.201300143

8 April 2023

Identifiers

DOI

10.1002/MINF.201300143

1 reference

release_5nuajf4ut5huxkeq4wjbsq4c4i

12 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/5nuajf4ut5huxkeq4wjbsq4c4i

mapped directly with Wikidata item

24 November 2022

based on heuristic

PubMed ID

27485570

1 reference

PubMed ID

27485570