CABS-dock protocols

View CABS-dock computational protocol

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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 in pipeline

2016
PMCID: 4860709
PMID: 27158082
DOI: 10.1038/srep25672

[…] by prosa, errat, and rampage servers., a molecular docking experiment was used to predict the interaction of h-sn1 with tnfr1 (protein database [pdb] code: 1tnr) and analyze the binding regions. cabs-dock was first used to predict the initial complex structure of tnfr1 with h-sn1; rosettadock was employed for further flexible docking majorization. pymol software was chosen to visualize […]


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CABS-dock in publications

 (11)
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 […]

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 […]

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 […]

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, […]

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 […]


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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].

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