PELE web server: atomistic study of biomolecular systems at your fingertips (Q30431383)

19 October 2017

PELE web server: atomistic study of biomolecular systems at your fingertips (English)

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19 October 2017

1 reference

2

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19 October 2017

Armin Madadkar-Sobhani

series ordinal

1

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PMC publication ID

3692087

19 October 2017

language of work or name

English

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publication date

31 May 2013

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19 October 2017

Nucleic Acids Research

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19 October 2017

41

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19 October 2017

Web Server issue

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19 October 2017

W322-8

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Creative Commons Attribution-NonCommercial 3.0 Unported

19 October 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Exploration of Protein Conformational Change with PELE and Meta-Dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Molecular interactions of prodiginines with the BH3 domain of anti-apoptotic Bcl-2 family members

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Single vs. multiple ligand pathways in globins: a computational view.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Kinetic characterization of the critical step in HIV-1 protease maturation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Identification of dual mTORC1 and mTORC2 inhibitors in melanoma cells: prodigiosin vs. obatoclax.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Identification of benzoxazin-3-one derivatives as novel, potent, and selective nonsteroidal mineralocorticoid receptor antagonists

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

How does a drug molecule find its target binding site?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

HexServer: an FFT-based protein docking server powered by graphics processors.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Prediction of side-chain conformations on protein surfaces

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Improved protein-ligand docking using GOLD

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

Anisotropy of fluctuation dynamics of proteins with an elastic network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3692087

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

20 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKT454

Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23729469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stereoselective hydride transfer by aryl-alcohol oxidase, a member of the GMC superfamily

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23729469

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT454

1 reference

journals/nar/Madadkar-SobhaniG13

19 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

3692087

19 October 2017

PubMed publication ID

23729469

1 reference

PMC publication ID

3692087