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Protocols

ArchiP specifications

Information


Unique identifier OMICS_24852
Name ArchiP
Alternative name Architectures of Proteins
Interface Web user interface
Restrictions to use None
Input data A 3D structure or a PDB ID.
Input format PDB
Programming languages FreePascal
Computer skills Basic
Version beta.1603061903
Stability Beta
Maintained Yes

Maintainers


  • person_outline Evgeniy Aksianov
  • person_outline Andrei Alexeevski

Additional information


http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip&page=help&data=alldocs

Information


Unique identifier OMICS_24852
Name ArchiP
Alternative name Architectures of Proteins
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages FreePascal
Computer skills Advanced
Version beta.1603061903
Stability Beta
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Evgeniy Aksianov
  • person_outline Andrei Alexeevski

Additional information


http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip&page=help&data=alldocs

Publication for Architectures of Proteins

ArchiP citations

 (17)
library_books

Plant Lectins and Lectin Receptor Like Kinases: How Do They Sense the Outside?

2017
Int J Mol Sci
PMCID: 5485988
PMID: 28561754
DOI: 10.3390/ijms18061164

[…] ded to intracellular kinase and trans-membrane domains to constitute receptor-like kinases, thus assigning CBMs as for classical lectins a role in signalling [,].In this review, we first describe the architectures of proteins harbouring C-type, G-type, L-type lectins, and LysM or malectin CBMs, and their distribution through kingdoms. The classification of lectins is based on their amino acid sequ […]

call_split

Putative extremely high rate of proteome innovation in lancelets might be explained by high rate of gene prediction errors

2016
Sci Rep
PMCID: 4967905
PMID: 27476717
DOI: 10.1038/srep30700
call_split See protocol

[…] e selected proteins were identified by the reciprocal best-hit method using NCBI’s non-redundant database of B. floridae proteins and the high quality, manually curated Swiss-Prot database.The domain architectures of proteins (defined as the linear sequence of Pfam-A domains) were determined using Pfam (http://pfam.xfam.org). Since Huang et al. used only Pfam-A domain types in their analyses we ha […]

library_books

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

2015
eLife
PMCID: 4501334
PMID: 26175406
DOI: 10.7554/eLife.06974.033

[…] es typical of Toxoplasma and Plasmodium micronemal secretory proteins. Examples include expansions of proteins containing SUSHI, EGF, TSP1, and vWA domains (data not shown). Chromerids possess unique architectures of proteins containing the macrophage perforin (MacPerf) domain (), which, previously found in apicomplexans and ciliates (as large expansions), are thought to function in apicomplexans […]

library_books

Large Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere

2014
PLoS Biol
PMCID: 3995644
PMID: 24756107
DOI: 10.1371/journal.pbio.1001843

[…] ty (71%) of these sequences fall into a length range of ∼190–275 residues, consistent with the size of biologically active cytGSTs. This conclusion is broadly consistent with Pfam predictions for the architectures of proteins in the cytGST superfamily. Only two other much smaller peaks occur in the histogram. In the first peak, comprising sequences of ∼300–350 residues in length, most were found t […]

library_books

The Evolution of Human Cells in Terms of Protein Innovation

2014
Mol Biol Evol
PMCID: 4032124
PMID: 24692656
DOI: 10.1093/molbev/mst139

[…] We have used phylogenetic stratification of the structural domain architectures of proteins expressed in FANTOM5 human cell samples to chart their histories in terms of protein innovation. The results show that human cell types, in the form that they currently exist […]

library_books

Earliest Holozoan Expansion of Phosphotyrosine Signaling

2013
Mol Biol Evol
PMCID: 4342544
PMID: 24307687
DOI: 10.1093/molbev/mst241

[…] Domain architectures of proteins containing the four pTyr signaling domains (TK catalytic, PTP catalytic, SH2, and PTB domains) were manually examined. The domain combinations occurring in these proteins wer […]


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ArchiP institution(s)
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
ArchiP funding source(s)
Supported, in part, by Russian Foundation of Basic Research, grants 13-07-00969 and 14-04-31709_mol_a.

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