ProCKSI protocols

ProCKSI specifications


Unique identifier OMICS_03668
Name ProCKSI
Alternative name Protein (Structure) Comparison, Knowledge, Similarity and Information
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages C++, Java, Perl
Computer skills Basic
Version 8.7.1
Stability Stable
Maintained Yes


  • Combinatorial Extension
  • FAST Alignment and Search Tool
  • Maximum Contact Map Overlap
  • ParsePDB
  • PDB Obsoletes
  • ProCKSI-Viz
  • qclust
  • SCOP
  • Universal Similarity Metric


  • person_outline Daniel Barthel <>
  • person_outline Jacek Blazewicz <>
  • person_outline Jonathan D. Hirst <>
  • person_outline Natalio Krasnogor <>
  • person_outline ProCKSI Team <>

Additional information

Publications for Protein (Structure) Comparison, Knowledge, Similarity and Information

ProCKSI IN pipelines

PMCID: 5290159
PMID: 28128207
DOI: 10.1038/ncomms14246

[…] structure was modelled using the archaeal p. abyssi nucs as a template using i-tasser16 and generated a reliable model (supplementary fig. 3). template and model were structurally aligned using the combinatorial extension (ce) algorithm17, built-in with pymol, to identify relevant residues. we used the structure-based alignment between this template and m. tuberculosis nucs (nucs_myctu) […]

PMCID: 3235984
PMID: 18389302
DOI: 10.1007/s00239-008-9075-7

[…] and hslv. bph from thiobacillus denitrificans has 22% sequence identity to the structure of hslv. we built a multiple sequence alignment from a multiple structural alignment for each cluster using combinatorial extension (shindyalov and bourne 1998) and built a tree using maximum likelihood (fig. 2). this was done to increase the quality of the alignment using structural information. anbu […]

ProCKSI institution(s)
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
ProCKSI funding source(s)
Supported by the Biotechnology and Biological Sciences Research Council (BBSRC) for grant BB/C511764/1, the Engineering and Physical Sciences Research Council (EPSRC) for grants GR/T07534/01 and EP/ D061571/1 and a grant from the Ministry of Higher Education in Poland.

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