Structure-based virtual screening for drug discovery: principles, applications and recent advances. (Q35282223)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

review article

1 reference

title

Structure-based virtual screening for drug discovery: principles, applications and recent advances (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

biomedical investigative technique

20 February 2020

main subject

drug screening

0 references

1 reference

19 September 2019

1 reference

28 September 2019

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2 October 2019

1 reference

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4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

author name string

Evanthia Lionta

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

George Spyrou

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

Demetrios K Vassilatis

series ordinal

3

1 reference

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20 February 2020

publication date

1 January 2014

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Current Topics in Medicinal Chemistry

20 February 2020

published in

5 references

20 June 2019

19 September 2019

28 September 2019

2 October 2019

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20 February 2020

volume

14

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20 February 2020

page(s)

1923-1938

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20 February 2020

issue

16

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Creative Commons Attribution-NonCommercial 3.0 Unported

20 February 2020

copyright license

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20 June 2019

19 September 2019

28 September 2019

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

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Multiple structures for virtual ligand screening: defining binding site properties-based criteria to optimize the selection of the query

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27 July 2018

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Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

27 July 2018

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27 July 2018

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Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton

27 July 2018

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Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model

27 July 2018

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FTMAP: extended protein mapping with user-selected probe molecules

27 July 2018

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Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

27 July 2018

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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

27 July 2018

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

27 July 2018

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Variability in docking success rates due to dataset preparation

27 July 2018

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Potential and limitations of ensemble docking

27 July 2018

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Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.

27 July 2018

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Structure-based virtual screening for drug discovery: a problem-centric review

27 July 2018

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Quantifying the chemical beauty of drugs.

27 July 2018

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Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

27 July 2018

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New developments on the cheminformatics open workflow environment CDK-Taverna

27 July 2018

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A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes

27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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

27 July 2018

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Targeting multifunctional proteins by virtual screening: structurally diverse cytohesin inhibitors with differentiated biological functions

27 July 2018

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27 July 2018

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27 July 2018

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New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays

27 July 2018

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Recipes for the selection of experimental protein conformations for virtual screening

27 July 2018

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A frequent kinase domain mutation that changes the interaction between PI3K and the membrane

27 July 2018

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Structure-based drug design strategies in medicinal chemistry

27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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27 July 2018

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Virtual screening - what does it give us?

27 July 2018

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27 July 2018

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Binding site detection and druggability index from first principles.

27 July 2018

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Discovery of human macrophage migration inhibitory factor (MIF)-CD74 antagonists via virtual screening

27 July 2018

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FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects

27 July 2018

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Physiochemical drug properties associated with in vivo toxicological outcomes

27 July 2018

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Towards improving compound selection in structure-based virtual screening

27 July 2018

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Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

27 July 2018

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Virtual screening and its integration with modern drug design technologies.

27 July 2018

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Drug discovery beyond the 'rule-of-five'.

27 July 2018

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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

27 July 2018

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Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups

27 July 2018

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

27 July 2018

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GLARE: a new approach for filtering large reagent lists in combinatorial library design using product properties

27 July 2018

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Very fast empirical prediction and rationalization of protein pKa values

27 July 2018

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Scalable molecular dynamics with NAMD

27 July 2018

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GROMACS: fast, flexible, and free

27 July 2018

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Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

27 July 2018

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27 July 2018

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The many roles of computation in drug discovery

27 July 2018

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Identifying specific kinase substrates through engineered kinases and ATP analogs

27 July 2018

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A ‘Rule of Three’ for fragment-based lead discovery?

27 July 2018

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Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

27 July 2018

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Molecular properties that influence the oral bioavailability of drug candidates

27 July 2018

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

27 July 2018

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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

27 July 2018

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Development and validation of a genetic algorithm for flexible docking

27 July 2018

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Comparative protein modelling by satisfaction of spatial restraints

27 July 2018

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VAMMPIRE: a matched molecular pairs database for structure-based drug design and optimization.

27 July 2018

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SFCscore(RF): a random forest-based scoring function for improved affinity prediction of protein-ligand complexes

26 September 2018

1 reference

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Ask the experts: past, present and future of the rule of five.

26 September 2018

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Molecular mechanism of SSR128129E, an extracellularly acting, small-molecule, allosteric inhibitor of FGF receptor signaling

26 September 2018

1 reference

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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

26 September 2018

1 reference

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FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.

26 September 2018

1 reference

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Considering the impact drug-like properties have on the chance of success

26 September 2018

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Consensus docking: improving the reliability of docking in a virtual screening context

26 September 2018

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Broad coverage of commercially available lead-like screening space with fewer than 350,000 compounds

26 September 2018

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Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Drug-likeness and increased hydrophobicity of commercially available compound libraries for drug screening.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

FRED and HYBRID docking performance on standardized datasets.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Surflex-Dock: Docking benchmarks and real-world application

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

CLEVER: pipeline for designing in silico chemical libraries.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Virtual screening in drug discovery -- a computational perspective

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

A fast flexible docking method using an incremental construction algorithm.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4443793

Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

26 September 2018

1 reference

12 December 2020

pK(a) based protonation states and microspecies for protein-ligand docking

1 reference

12 December 2020

Computer-aided drug design platform using PyMOL

1 reference

12 December 2020

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

1 reference

12 December 2020

10.2174/1568026614666140929124445

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25262799%20AND%20SRC:MED&resulttype=core&format=json