CABS-dock statistics

info info

Citations per year

info

Popular tool citations

chevron_left Protein-peptide docking chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

CABS-dock specifications

Information


Unique identifier OMICS_08324
Name CABS-dock
Interface Web user interface
Restrictions to use None
Input data Protein receptor structure in the PDB format or protein PDB code along with the chain identifier(s) and peptide sequence
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Sebastian Kmiecik

Additional information


http://biocomp.chem.uw.edu.pl/CABSdock/tutorial http://biocomp.chem.uw.edu.pl/CABSdock/learn_more

Publications for CABS-dock

CABS-dock citations

 (11)
library_books

Improved scFv Anti LOX 1 Binding Activity by Fusion with LOX 1 Binding Peptides

2017
Biomed Res Int
PMCID: 5637825
PMID: 29094051
DOI: 10.1155/2017/8946935

[…] was performed using the automated initial stage docking algorithm implemented by zdock (http://zdock.umassmed.edu/) []. docking of the lox-1-binding peptides to the lox-1 protein was performed using cabs-dock (http://biocomp.chem.uw.edu.pl/cabsdock/) []. for all the original models, energy minimization and 30 ns molecular dynamic simulations were performed using standard gromos96 43a2 force […]

library_books

An alternate mode of oligomerization for E. coli SecA

2017
Sci Rep
PMCID: 5603524
PMID: 28924213
DOI: 10.1038/s41598-017-11648-5

[…] orientations while maintaining the same interactions with the n-terminus, in this case modelled into the groove between nbd1 and nbd2 which was identified as a peptide binding “hotspot” using the cabs-dock server,. with this type of interaction, the c-terminal domains could adopt different relative orientations, possibly explaining why the exact solution structure of the seca dimer […]

library_books

Phage Displayed Peptides Selected to Bind Envelope Glycoprotein Show Antiviral Activity against Dengue Virus Serotype 2

2017
PMCID: 5610824
PMID: 29081802
DOI: 10.1155/2017/1827341

[…] structurally closely related to several viral envelope glycoproteins in the pdb database. to study the probable binding mode of the active peptides, we performed computational docking analysis using cabs-dock web server with the default parameters except for the increase of simulation cycles to 200 []. the best poses, ranked according to trajectory characteristics, were further analyzed […]

library_books

A protocol for CABS dock protein–peptide docking driven by side chain contact information

2017
Biomed Eng Online
PMCID: 5568604
PMID: 28830545
DOI: 10.1186/s12938-017-0363-6

[…] technique with external information about side-chain contacts to sample and select the best possible models., in this paper we test a new protocol that uses information about side-chain contacts in cabs-dock protein–peptide docking. as shown in our recent studies, cabs-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. however, […]

library_books

Understanding Russell’s viper venom factor V activator’s substrate specificity by surface plasmon resonance and in silico studies

2017
PLoS One
PMCID: 5521794
PMID: 28732041
DOI: 10.1371/journal.pone.0181216

[…] more number of interactions is found in either side of the p0 site; accordingly, it may act on either the substrate or the inhibitor. a model for the peptide i and ii was designed using the server cabs-dock, which builds the model as well as performed docking with the protein., the spr is a well-known primary protein-ligand screening method for the measurement of a real-time, label-free […]

library_books

The pepATTRACT web server for blind, large scale peptide–protein docking

2017
Nucleic Acids Res
PMCID: 5570166
PMID: 28460116
DOI: 10.1093/nar/gkx335

[…] have to be fully blind, and run to completion within a few minutes, preferably as a web server. recently, several new fully blind protein–peptide docking methods have been published: anchordock (), cabs-dock () and mdockpep (). of these, only cabs-dock is available as a web server. unfortunately, current fully blind methods are too slow for large-scale applications. pepattract, anchordock […]


Want to access the full list of citations?
CABS-dock institution(s)
Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland; Faculty of Physics, University of Warsaw, Warsaw, Poland
CABS-dock funding source(s)
Supported by the National Science Center (NCN, Poland) Grant [MAESTRO2014/14/A/ ST6/00088].

CABS-dock reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CABS-dock