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Protocols

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

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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 citations

 (37)
library_books

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1

2018
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 […]

library_books

Building protein protein interaction networks for Leishmania species through protein structural information

2018
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 […]

library_books

Exploring the inhibition mechanism of adenylyl cyclase type 5 by n terminal myristoylated Gαi1

2017
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 […]

library_books

Fungal Hybrid B heme peroxidases – unique fusions of a heme peroxidase domain with a carbohydrate binding domain

2017
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 […]

library_books

Enriching Traditional Protein protein Interaction Networks with Alternative Conformations of Proteins

2017
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 […]

library_books

A receptor dependent 4D QSAR approach to predict the activity of mutated enzymes

2017
PMCID: 5524700
PMID: 28740233
DOI: 10.1038/s41598-017-06625-x

[…] generating cep. 1000 conformations of the enzyme active site complexed with the substrate; each conformation pertaining to 1 ps of the md simulation were structurally aligned using the program do_multiprot. the aligned e-s reaction coordinates are called as cep. the ceps of the 6 enzyme variants including the wild type were inserted into the lqtagrid module to generate the interaction energy […]


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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.

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