Scoring ensembles of docked protein:ligand interactions for virtual lead optimization (Q42920364)

11 November 2017

Scoring ensembles of docked protein:ligand interactions for virtual lead optimization (English)

1 reference

11 November 2017

Janet L Paulsen

1

1 reference

PMCID

2819002

11 November 2017

Amy C Anderson

series ordinal

2

1 reference

11 November 2017

1 December 2009

1 reference

Journal of Chemical Information and Modeling

11 November 2017

1 reference

11 November 2017

49

1 reference

11 November 2017

12

1 reference

11 November 2017

2813-2819

1 reference

In vitro biological activity and structural analysis of 2,4-diamino-5-(2'-arylpropargyl)pyrimidine inhibitors of Candida albicans.

11 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Evaluating docking methods for prediction of binding affinities of small molecules to the G protein betagamma subunits

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Probing the Active Site ofCandida glabrataDihydrofolate Reductase with High Resolution Crystal Structures and the Synthesis of New Inhibitors

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Synthetic and Crystallographic Studies of a New Inhibitor Series Targeting Bacillus anthracis Dihydrofolate Reductase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Structure-based approach to the development of potent and selective inhibitors of dihydrofolate reductase from cryptosporidium

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Structure-Guided Development of Efficacious Antifungal Agents Targeting Candida glabrata Dihydrofolate Reductase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Scoring functions for protein-ligand docking

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Parameter estimation for scoring protein-ligand interactions using negative training data

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Design and synthesis of benzoic acid derivatives as influenza neuraminidase inhibitors using structure-based drug design

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

X-ray crystallographic studies of Candida albicans dihydrofolate reductase. High resolution structures of the holoenzyme and an inhibited ternary complex

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Molecular docking to ensembles of protein structures

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2819002

Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

1 December 2018

1 reference

12 December 2020

Sialidase inhibitors related to zanamivir: synthesis and biological evaluation of 4H-pyran 6-ether and ketone

1 reference

12 December 2020

Highly efficient ligands for dihydrofolate reductase from Cryptosporidium hominis and Toxoplasma gondii inspired by structural analysis

1 reference

12 December 2020

Improving database enrichment through ensemble docking

1 reference

12 December 2020

Predicting free energy changes using structural ensembles

1 reference

12 December 2020

Identifiers

DOI

10.1021/CI9003078

1 reference

journals/jcisd/PaulsenA09

11 November 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

11 November 2017

1 reference

PMCID

2819002