ProCKSI protocols

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ProCKSI specifications

Information


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

Subtools


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

Maintainers


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

Additional information


https://projects.ico2s.org/projects/procksi/

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

ProCKSI in pipeline

2013
PMCID: 3578447
PMID: 23440025
DOI: 10.3389/fmicb.2012.00419

[…] ligand binding residues and is likely a “nif-like” protein which are conserved in methanogenic archaea ()., inferred structures were compared using an “all against all” comparison performed by the procksi server. the relatedness of structures was calculated with standardized distance matrix derived from the vorolign v-score () and hierarchical clustering accomplished using the complete link […]


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ProCKSI in publications

 (20)
PMCID: 5753887
PMID: 29317803
DOI: 10.1177/1177932217747277

[…] of sa-mot and phyre2 servers were used. the normal mode of phyre 2 server that models structures based on a single template was implemented. multiple structural alignment was investigated through procksi server where different tools were used to analyze the predicted protein structures. parameters of procksi server were set to default settings. these structures were then searched […]

PMCID: 4641208
PMID: 26605332
DOI: 10.1155/2015/563674

[…] and parallel processing capabilities they offer []., in this work, we extend the framework presented in [] for mcpsc. we augment the software with implementations of two popularly used psc methods—combinatorial extension (ce) [] and universal similarity metric (usm) []—in addition to tmalign [], and then combine them to create a scalable mcpsc application for the scc. we also develop […]

PMCID: 4416183
PMID: 25916734
DOI: 10.1186/1471-2105-16-S6-S2

[…] sequences expressed both in terms of classic evolutionary models [,], and in terms of compression-based models [,], that derive their theoretic assumption from the information theory concepts of universal similarity metric []. the compression-based approaches have been also adopted for the study of phylogenetic relationships among animal species, considering the barcode coi gene [,]., recent […]

PMCID: 4344357
PMID: 25723922
DOI: 10.1107/S1600577515002131

[…] occupancy was 1. if multiple conformations were available, they were replaced by the first conformation with the highest occupancy. the processed pdb files were subsequently parsed (interpreted) by parsepdb (bulheller & hirst, 2009) to extract the chain information, atomic coordinates and atomic b-factors. further perl scripts were written to extract and calculate ancillary information, […]

PMCID: 3980841
PMID: 24779008
DOI: 10.1155/2014/309650

[…] in the hash table-based algorithm include seqmap [], pass [], maq [], gassst [], rmap [], perm [], razers [, ], microread fast alignment search tool (mrfast) [], microread (substitutions only) fast alignment and search tool (mrsfast) [], genomemapper [], and boat []., however, diverse strategies for seeds detection cause a distinction among multiple alignment algorithms. to handle […]


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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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