(Q28478200)

2

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Giovanni Bottegoni

object named as

Giovanni Bottegoni

1

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author name string

Manuel Rueda

3

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Andrea Cavalli

Optimal assignment methods for ligand-based virtual screening

5

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language of work or name

English

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publication date

2011

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published in

PLOS One

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volume

6

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issue

5

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page(s)

e18845

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Flexible ligand docking to multiple receptor conformations: a practical alternative

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Flexible ligand docking using conformational ensembles

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Recommendations for evaluation of computational methods

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

A critical assessment of docking programs and scoring functions

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Benchmarking sets for molecular docking

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Molecular docking screens using comparative models of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Novel trends in high-throughput screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

The flexible pocketome engine for structural chemogenomics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

The future of high-throughput screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate 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=3098722

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Exploring experimental sources of multiple protein conformations in structure-based drug design.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Evaluation of the utility of homology models in high throughput 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=3098722

Ensemble docking of multiple protein structures: considering protein structural variations in 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=3098722

Docking and scoring--theoretically easy, practically impossible?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Virtual ligand screening: strategies, perspectives and limitations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3beta 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=3098722

Target flexibility in molecular recognition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Virtual screening of chemical libraries

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Testing a flexible-receptor docking algorithm in a model binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

The many roles of computation in drug 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=3098722

Conformational flexibility models for the receptor in structure based drug design.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Implications of protein flexibility for drug 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=3098722

Nuclear hormone receptor targeted virtual screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

How does consensus scoring work for virtual library screening? An idealized computer experiment

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

High-throughput docking for lead generation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Accommodating protein flexibility in computational drug design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Recipes for the selection of experimental protein conformations for virtual screening

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

Molecular docking to ensembles of protein structures

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3098722

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

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Comparative assessment of scoring functions on a diverse test set.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Assessing scoring functions for protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Protein-ligand docking against non-native protein conformers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Virtual screening using protein-ligand docking: avoiding artificial enrichment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

FLIPDock: docking flexible ligands into flexible receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018845

Recognition of distantly related proteins through energy calculations

21 January 2018

1 reference

12 December 2020

Protocols for bridging the peptide to nonpeptide gap in topological similarity searches

1 reference

12 December 2020

Improving database enrichment through ensemble docking

1 reference

12 December 2020

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

1 reference

12 December 2020