MultiProt protocols

View MultiProt computational protocol

MultiProt statistics

You need an account to access this content

info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Multiple structure alignment chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

MultiProt specifications

Information


Unique identifier OMICS_04207
Name MultiProt
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Maxim Shatsky <>

Information


Unique identifier OMICS_04207
Name MultiProt
Interface Web user interface
Restrictions to use None
Input data PDB ID
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Maxim Shatsky <>

Publication for MultiProt

MultiProt in pipelines

 (4)
2016
PMCID: 4777378
PMID: 26939122
DOI: 10.1371/journal.pone.0150404

[…] superimposition of the two domains. structural superimposition, manual inspection and trimming of the models was done using pymol []., the resulting domain structures were superimposed (using multiprot 1.6 []) with homologous domain from a crystallographic structure pdb id: 3e0d [] (one of templates used in homology modeling) and the 38 bp length dna fragment close to the superimposed […]

2014
PMCID: 4184797
PMID: 25279835
DOI: 10.1371/journal.pone.0108415

[…] 1.3, schrödinger, llc) for secondary structure and side chain analysis. in addition comparative analysis of the mup family employed promals3d , for secondary structure driven sequence alignment and multiprot for homologous structure alignment. random coil index (rci) analysis was through the rci webserver . the castp programme was used to measure cavity size and the programmes pic , pdbepisa […]

2012
PMCID: 3441751
PMID: 23028322
DOI: 10.1371/journal.ppat.1002923

[…] built using topdraw . characterization of the domain fold was carried out using scop ; alignment of the cs-domain family employed promals3d for secondary structure-driven sequence alignment and multiprot for homologous structure alignment. random coil index (rci) analysis was carried out using the rci webserver ., the structure of the n1 domain (n1pilq419–514) could not be determined using […]

2011
PMCID: 3127847
PMID: 21738568
DOI: 10.1371/journal.pone.0019521

[…] building and automated building with arp-warp . final refinement cycles were done with refmac5., models were validated with molprobity . initial structure based sequence alignments were made with multiprot and staccato using pdb entries 3p0l, 1ln1, 1em2, 1jss, 2r55, 2e30, 2pso and 3fo5. the alignment was edited with bodil (similarity matrix strmat110; minor manual edits) to include full […]

MultiProt in publications

 (37)
PMCID: 5934628
PMID: 29660015
DOI: 10.1093/nar/gky256

[…] in coot and refined using phenix () to final rwork/rfree of 0.170/0.217. data collection and refinement statistics are shown in table ., structures of val1-b3 and related domains were overlaid using multiprot (). structure-based sequence alignments were generated using the staccato algorithm () and espript (). structures were visualized and figures generated using pymol (the pymol molecular […]

PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] 4.0.2., the prism protocol requires as input atomic coordinates of two proteins, and a template set formed by pairs of proteins that are known to interact. this tool applies the naccess [] and multiprot [] softwares to compare the residues responsible for the interaction in the template set with the surface residues of a pair of target proteins, and then prism protocol uses […]

PMCID: 5608429
PMID: 28892485
DOI: 10.1371/journal.pcbi.1005673

[…] was solvated in 30 000 water molecules and a 150 mm kcl concentration. the initial location of the mg2+ ion in the active site of the enzyme was the same as in the gαi1myr:ac5 complex system., multiprot [] and vmd [] were used to align protein structures. uniprot [] was used to align protein sequences. images were prepared with vmd []., the stability of the docked gαi1myr:ac5 complex […]

PMCID: 5571214
PMID: 28839281
DOI: 10.1038/s41598-017-09581-8

[…] experimental 3d structure were created with the phyre-2 server (http://www.sbg.bio.ic.ac.uk/phyre2/) employing the “normal” modelling mode. obtained structures were superimposed using the program multiprot (http://bioinfo3d.cs.tau.ac.il/multiprot/) and displayed with the weblab viewer lite programme (accelrys inc.)., of all peroxidases used in this work can be retrieved in peroxibase10 […]

PMCID: 5543104
PMID: 28775330
DOI: 10.1038/s41598-017-07351-0

[…] different protein structures. prism algorithm consists of four steps. in the first step, it extracts the surfaces of target proteins. then, it splits the template interfaces into two sides and using multiprot it calculates the similarity of each template interface side to the target protein surfaces in the second step. multiprot can find the structural similarities of proteins […]

MultiProt institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick, Inc. Laboratory of Experimental and Computational Biology, NCI-Frederick Frederick, MD, USA
MultiProt funding source(s)
Supported by the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

MultiProt reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MultiProt