(Q37296002)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

review article

3 references

8 April 2021

22 August 2022

Docking, virtual high throughput screening and in silico fragment-based drug design (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

biomedical investigative technique

20 January 2020

main subject

drug screening

0 references

1 reference

19 September 2019

computational biology

1 reference

8 April 2021

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

3

Olivier Michielin

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

author name string

Vincent Zoete

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

language of work or name

1 reference

21 January 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

Journal of Cellular and Molecular Medicine

20 January 2020

1 February 2009

2 references

8 April 2021

22 August 2022

4 references

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

8 April 2021

22 August 2022

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

page(s)

238-248

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

Recent developments in fragment-based drug discovery

20 January 2020

cites work

1 reference

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Fragment-based de novo ligand design by multiobjective evolutionary optimization

6 September 2017

1 reference

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Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model

6 September 2017

1 reference

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Theoretical and practical considerations in virtual screening: a beaten field?

6 September 2017

1 reference

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Virtual screening strategies in drug discovery

6 September 2017

1 reference

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A semiempirical free energy force field with charge-based desolvation

6 September 2017

1 reference

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Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking

6 September 2017

1 reference

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Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

6 September 2017

1 reference

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A critical assessment of docking programs and scoring functions

6 September 2017

1 reference

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Protein-ligand docking: current status and future challenges

6 September 2017

1 reference

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Virtual ligand screening: strategies, perspectives and limitations

6 September 2017

1 reference

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MolDock: a new technique for high-accuracy molecular docking

6 September 2017

1 reference

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Structure-based virtual screening of chemical libraries for drug discovery

6 September 2017

1 reference

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Computer-based de novo design of drug-like molecules

6 September 2017

1 reference

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Fragment-based lead discovery: leads by design

6 September 2017

1 reference

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Comparing protein-ligand docking programs is difficult.

6 September 2017

1 reference

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Navigating chemical space for biology and medicine

6 September 2017

1 reference

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

6 September 2017

1 reference

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

6 September 2017

1 reference

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High-throughput docking as a source of novel drug leads

6 September 2017

1 reference

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Pursuing the leadlikeness concept in pharmaceutical research.

6 September 2017

1 reference

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Comparative study of several algorithms for flexible ligand docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

The many roles of computation in drug discovery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Improved protein-ligand docking using GOLD

6 September 2017

1 reference

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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

6 September 2017

1 reference

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Molecular recognition and docking algorithms

6 September 2017

1 reference

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Trends in virtual combinatorial library design

6 September 2017

1 reference

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A new test set for validating predictions of protein-ligand interaction.

6 September 2017

1 reference

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A review of protein-small molecule docking methods

6 September 2017

1 reference

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PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors

6 September 2017

1 reference

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Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design

6 September 2017

1 reference

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Ligand-protein database: linking protein-ligand complex structures to binding data

6 September 2017

1 reference

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Pharmacophore modeling and three-dimensional database searching for drug design using catalyst

6 September 2017

1 reference

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Molecular complexity and its impact on the probability of finding leads for drug discovery

6 September 2017

1 reference

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

6 September 2017

1 reference

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FlexE: efficient molecular docking considering protein structure variations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Efficient electrostatic solvation model for protein-fragment docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

RECAP--retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Development and validation of a genetic algorithm for flexible docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

The art and practice of structure-based drug design: A molecular modeling perspective

6 September 2017

1 reference

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HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules

6 September 2017

1 reference

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A geometric approach to macromolecule-ligand interactions

6 September 2017

1 reference

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

6 September 2017

1 reference

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6 September 2017

2 references

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6 September 2017

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Discovery of a nanomolar inhibitor of the human murine double minute 2 (MDM2)-p53 interaction through an integrated, virtual database screening strategy.

21 January 2018

1 reference

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The properties of known drugs. 1. Molecular frameworks

14 September 2017

1 reference

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

28 September 2017

1 reference

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QXP: powerful, rapid computer algorithms for structure-based drug design.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Computational combinatorial ligand design: application to human alpha-thrombin.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

An automated method for dynamic ligand design.

26 June 2018

1 reference

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Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Automated site-directed drug design: the prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Protein-ligand docking against non-native protein conformers

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Chemical fragment spaces for de novo design.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Generation and selection of novel estrogen receptor ligands using the de novo structure-based design tool, SkelGen.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

LEA3D: a computer-aided ligand design for structure-based drug design.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Virtual screening for inhibitors of human aldose reductase.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Protein flexibility in ligand docking and virtual screening to protein kinases.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Characteristic physical properties and structural fragments of marketed oral drugs.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Comparative evaluation of 11 scoring functions for molecular docking

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

A genetic algorithm for structure-based de novo design

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Knowledge-based scoring function to predict protein-ligand interactions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Feature trees: a new molecular similarity measure based on tree matching.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

A comparison of heuristic search algorithms for molecular docking.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

A fast flexible docking method using an incremental construction algorithm.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

SPROUT: a program for structure generation.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

BUILDER v.2: improving the chemistry of a de novo design strategy.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

Functionality maps of binding sites: a multiple copy simultaneous search method

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3823351

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

3 September 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

Sulfonylureas and Glinides Exhibit Peroxisome Proliferator-Activated Receptor Activity: A Combined Virtual Screening and Biological Assay Approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

21 January 2018

How many leads from HTS?

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

Virtual screening—an overview

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1582-4934.2008.00665.X

Structure and reaction based evaluation of synthetic accessibility

21 January 2018

1 reference

12 December 2020

SYNOPSIS: SYNthesize and OPtimize System in Silico

1 reference

12 December 2020

CONCERTS: dynamic connection of fragments as an approach to de novo ligand design

1 reference

12 December 2020

Properties of known drugs. 2. Side chains

1 reference

12 December 2020

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

Chemical space and biology

1 reference

12 December 2020

Virtual exploration of the small-molecule chemical universe below 160 Daltons

1 reference

12 December 2020

Binding MOAD (Mother Of All Databases)

1 reference

12 December 2020

On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure

1 reference

12 December 2020

10.1111/J.1582-4934.2008.00665.X

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19183238%20AND%20SRC:MED&resulttype=core&format=json

20 January 2020

1 reference