Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol (Q34595676)

3 August 2017

title

Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol (English)

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3 August 2017

0 references

1 reference

Tian Zhu

1

1 reference

3 August 2017

Hyun Lee

2

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3 August 2017

Hao Lei

3

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3 August 2017

Christopher Jones

4

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3 August 2017

Kavankumar Patel

5

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3 August 2017

Michael E Johnson

6

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3 August 2017

Kirk E Hevener

7

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3 August 2017

publication date

14 March 2013

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Journal of Chemical Information and Modeling

3 August 2017

published in

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3 August 2017

volume

53

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3 August 2017

issue

3

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3 August 2017

page(s)

560-572

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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

3 August 2017

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7 July 2018

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7 July 2018

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A Practical Use of Ligand Efficiency Indices Out of the Fragment-Based Approach: Ligand Efficiency-Guided Lead Identification of Soluble Epoxide Hydrolase Inhibitors

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Investigation of MM-PBSA rescoring of docking poses

7 July 2018

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Nucleotide biosynthesis is critical for growth of bacteria in human blood

7 July 2018

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

7 July 2018

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Bias, reporting, and sharing: computational evaluations of docking methods

7 July 2018

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Molecular dynamics simulations and their application to four-stranded DNA.

7 July 2018

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Molecular evolution of affinity and flexibility in the immune system

7 July 2018

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N 5 -CAIR Mutase: Role of a CO 2 Binding Site and Substrate Movement in Catalysis † , ‡

7 July 2018

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Drugs for bad bugs: confronting the challenges of antibacterial discovery

7 July 2018

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A critical assessment of docking programs and scoring functions

7 July 2018

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Measuring diagnostic and predictive accuracy in disease management: an introduction to receiver operating characteristic (ROC) analysis

7 July 2018

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7 July 2018

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Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Ligand efficiency: a useful metric for lead selection

7 July 2018

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Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy

7 July 2018

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Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway

7 July 2018

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Large-scale identification of virulence genes from Streptococcus pneumoniae.

7 July 2018

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Development and validation of a genetic algorithm for flexible docking

7 July 2018

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Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection.

7 July 2018

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Reactions catalyzed by 5-aminoimidazole ribonucleotide carboxylases from Escherichia coli and Gallus gallus: a case for divergent catalytic mechanisms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Growth in mouse peritoneal macrophages of Yersinia pestis lacking established virulence determinants.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Effect of different purine auxotrophic mutations on mouse-virulence of a Vi-positive strain of Salmonella dublin and of two strains of Salmonella typhimurium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Mechanisms of cooperativity and allosteric regulation in proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

De novo purine nucleotide biosynthesis: cloning, sequencing and expression of a chicken PurH cDNA encoding 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase-IMP cyclohydrolase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Docking performance of fragments and druglike compounds.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

QM/MM as a tool in fragment based drug discovery. A cross-docking, rescoring study of kinase inhibitors

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3752004

The growth of purine mutants of Bacillus anthracis in the body of the mouse

27 October 2018

1 reference

12 December 2020

Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4

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Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules

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Free energy calculations of glycosaminoglycan-protein interactions

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Healthcare-associated infection and antimicrobial resistance: moving beyond description to prevention

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Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring

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Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature‐tagged mutagenesis

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Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes

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12 December 2020

Identifiers

DOI

10.1021/CI300502H

1 reference

journals/jcisd/ZhuLLJPJH13

3 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 August 2017

1 reference