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ProTop specifications

Information


Unique identifier OMICS_24855
Name ProTop
Alternative name Protein Topologies
Interface Web user interface
Restrictions to use None
Input data Two protein structures or two PDB ID.
Input format PDB
Computer skills Basic
Version beta.1603061903
Stability Beta
Maintained Yes

Maintainer


  • person_outline Evgeniy Aksianov <>

ProTop in publications

 (58)
PMCID: 5865747
PMID: 29570745
DOI: 10.1371/journal.pone.0194945

[…] blast function at http://knowpulse.usask.ca., the deduced amino acid sequences of the putative lcmlo genes were analyzed by several prediction programs to identify functional domains, to determine protein topologies, and sub-cellular localizations [–]. the prediction programs were run with default settings of the online servers listed in . the cds sequences of the annotated mlo genes in lentil […]

PMCID: 5845226
PMID: 29523074
DOI: 10.1186/s12866-018-1157-0

[…] protein [, , –]. in addition, a careful examination of at least three databases revealed that some proteins were predicted to have transmembrane domains (tmd) and a peptide signal (signal p). these protein topologies suggested that the putative proteins are anchored to a membrane (table  and additional files and : tables: s3 and s5)., the pas domain appears to be prevalent in proteins involved […]

PMCID: 5834214
PMID: 29462184
DOI: 10.1371/journal.ppat.1006892

[…] were identified as prominent hits in our np interactome. the mammalian cct is critical for folding of many proteins with important functions in diverse cellular processes [], and may protect complex protein topologies within its central cavity during biosynthesis and folding []. the contribution of cct members to np assembly into a nucleocapsid structure could account for their presence […]

PMCID: 5855793
PMID: 29443891
DOI: 10.3390/ijms19020571

[…] in a cubic box with each side equal to 6 nm and neutralized by counterions. each system consisted of about 21,000 interacting particles. , the amber99sb-ildn force field [] was used to define protein topologies and the tip3p model [] was used to represent the water molecules. the systems were first minimized by applying the steepest descent energy minimization algorithm, followed […]

PMCID: 5821083
PMID: 29440573
DOI: 10.1128/mBio.02267-17

[…] the absence of a universally conserved proline in colm domains (see above). the interacting chaperone(s) may ultimately define which type of immunity partner is required. (ii) different immunity protein topologies may point to immunity at different cellular locations, i.e., fundamentally different mechanisms would exist to impede lipid ii-degrading activity, targeting different patches […]


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ProTop institution(s)
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
ProTop 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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