CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures (Q28484476)

5

0 references

Jiří Damborský

object named as

Jiri Damborsky

13

0 references

Barbora Kozlíková

6

object named as

Barbora Kozlikova

0 references

author name string

Eva Chovancova

1

0 references

Antonin Pavelka

2

0 references

Petr Benes

3

0 references

Ondrej Strnad

4

0 references

Artur Gora

7

0 references

Vilem Sustr

8

0 references

Petr Medek

10

0 references

Lada Biedermannova

11

0 references

Jiri Sochor

PLOS Computational Biology

12

0 references

language of work or name

English

0 references

publication date

2012

0 references

published in

0 references

volume

8

0 references

issue

10

0 references

page(s)

e1002708

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

18 October 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Structure and gating mechanism of the acetylcholine receptor pore

19 March 2017

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Molecular dynamics of acetylcholinesterase

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Crystal structure and mechanism of a calcium-gated potassium channel

19 March 2017

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Channeling of ammonia in glucosamine-6-phosphate synthase

19 March 2017

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Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair

19 March 2017

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The Structure of the Potassium Channel: Molecular Basis of K + Conduction and Selectivity

19 March 2017

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Coupled Formation of an Amidotransferase Interdomain Ammonia Channel and a Phosphoribosyltransferase Active Site,

19 March 2017

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VMD: visual molecular dynamics

19 March 2017

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Purification and properties of haloalkane dehalogenase from Corynebacterium sp. strain m15-3

19 March 2017

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Identification of new, well-populated amino-acid sidechain rotamers involving hydroxyl-hydrogen atoms and sulfhydryl-hydrogen atoms

19 March 2017

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CAVER: a new tool to explore routes from protein clefts, pockets and cavities

7 April 2017

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HOLE: a program for the analysis of the pore dimensions of ion channel structural models

7 April 2017

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Protein dynamics and ligand migration interplay as studied by computer simulation.

7 April 2017

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3V: cavity, channel and cleft volume calculator and extractor

29 September 2017

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The gates of ion channels and enzymes

29 September 2017

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Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

29 September 2017

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PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure

29 September 2017

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A substrate channel in the nitrogenase MoFe protein

29 September 2017

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Finding and characterizing tunnels in macromolecules with application to ion channels and pores.

29 September 2017

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Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems.

29 September 2017

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MolAxis: a server for identification of channels in macromolecules

29 September 2017

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MolAxis: efficient and accurate identification of channels in macromolecules

29 September 2017

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Structure and function of the bacterial Sec translocon.

29 September 2017

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What common structural features and variations of mammalian P450s are known to date?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

The ins and outs of cytochrome P450s.

29 September 2017

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Principles of selective ion transport in channels and pumps

29 September 2017

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Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A.

29 September 2017

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Protein engineering of toluene 4-monooxygenase of Pseudomonas mendocina KR1 for synthesizing 4-nitrocatechol from nitrobenzene

29 September 2017

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29 September 2017

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Enzymes with molecular tunnels

29 September 2017

1 reference

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Blocking the tunnel: engineering of Candida rugosa lipase mutants with short chain length specificity

29 September 2017

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Molecular dynamics simulations of biomolecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Channeling of substrates and intermediates in enzyme-catalyzed reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Aquaporin water channels: unanswered questions and unresolved controversies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Ile115Leu mutation in the SRS1 region of an insect cytochrome P450 (CYP6B1) compromises substrate turnover via changes in a predicted product release channel

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Exploring coumarin egress channels in human cytochrome p450 2a6 by random acceleration and steered molecular dynamics simulations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

HaloTag: a novel protein labeling technology for cell imaging and protein analysis

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3475669

An engineered blockage within the ammonia tunnel of carbamoyl phosphate synthetase prevents the use of glutamine as a substrate but not ammonia

27 November 2018

1 reference

12 December 2020

Purification and characterization of a bacterial dehalogenase with activity toward halogenated alkanes, alcohols and ethers

1 reference

12 December 2020

Isolation and characterization of a haloalkane halidohydrolase from Rhodococcus erythropolis Y2

1 reference

12 December 2020

Site‐directed mutagenesis of the lower parts of the major substrate channel of yeast catalase A leads to highly increased peroxidatic activity

1 reference

12 December 2020

HOLLOW: generating accurate representations of channel and interior surfaces in molecular structures

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1002708

Identifiers

DOI

1 reference

journals/ploscb/ChovancovaPBSBKGSKMBSD12

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

23093919

1 reference