MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels (Q36088495)

12 August 2017

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels (English)

1 reference

12 August 2017

10

Michal Otyepka

0 references

Crina-Maria Ionescu

7

Crina-Maria Ionescu

0 references

Radka Svobodová Vařeková

8

Radka Svobodová Vareková

1 reference

12 August 2017

David Sehnal

3

0 references

Karel Berka

Karel Berka

1

0 references

Jaroslav Koča

Jaroslav Koca

9

0 references

Veronika Navrátilová

5

Veronika Navrátilová

1 reference

12 August 2017

Ondrej Hanák

2

1 reference

12 August 2017

Pavel Banás

4

1 reference

12 August 2017

Deepti Jaiswal

6

1 reference

12 August 2017

language of work or name

English

0 references

publication date

2 May 2012

1 reference

12 August 2017

Nucleic Acids Research

1 reference

12 August 2017

40

1 reference

12 August 2017

Web Server issue

1 reference

12 August 2017

W222-7

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

12 August 2017

start time

5 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Biomolecules in the computer: Jmol to the rescue

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

dxTuber: detecting protein cavities, tunnels and clefts based on protein and solvent dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Interactions of cytochrome P450s with their ligands

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

HotSpot Wizard: a web server for identification of hot spots in protein engineering.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

MolAxis: a server for identification of channels in macromolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

MolAxis: efficient and accurate identification of channels in macromolecules

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Structural characteristics of channels and pathways in photosystem II including the identification of an oxygen channel

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The ins and outs of cytochrome P450s.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Principles of selective ion transport in channels and pumps

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

A survey of active site access channels in cytochromes P450.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Voronoi and Voronoi-related tessellations in studies of protein structure and interaction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Crystal structure and mechanism of a calcium-gated potassium channel

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Cytochromes P450 and metabolism of xenobiotics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The importance of aquaporin water channel protein structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

2 October 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The three-dimensional structure of human erythrocyte aquaporin CHIP

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

A simple method for displaying the hydropathic character of a protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The interpretation of protein structures: Total volume, group volume distributions and packing density

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The rapid generation of mutation data matrices from protein sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

The characterization of amino acid sequences in proteins by statistical methods

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3394309

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

23 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS363

A note on two problems in connexion with graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS363

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS363

The Geometry of the Ribosomal Polypeptide Exit Tunnel

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKS363

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

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22553366

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Hydrophobicity and structural classes in proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22553366

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKS363

1 reference

journals/nar/BerkaHSBNJIVKO12

12 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 August 2017

1 reference