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XtalPred specifications

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Unique identifier OMICS_11908
Name XtalPred
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Protein sequence(s) (up to 5000 residues per sequence, 10 sequences per submission)
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No

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Publication for XtalPred

XtalPred citations

 (20)
library_books

Dynamic localization of a yeast development–specific PP1 complex during prospore membrane formation is dependent on multiple localization signals and complex formation

2017
Mol Biol Cell
PMCID: 5739302
PMID: 29046399
DOI: 10.1091/mbc.E17-08-0521

[…] during image collection. three-dimensional stacks were performed with iplab 3.6.5a., jpred4 (http://www.compbio.dundee.ac.uk/jpred4/index.html), psipred (http://bioinf.cs.ucl.ac.uk/psipred/), and xtalpred (http://ffas.burnham.org/xtalpred-cgi/xtal.pl) were used to predict the secondary structure of gip1. heliquest (http://heliquest.ipmc.cnrs.fr/) was used to predict the structure […]

library_books

PP2A B′ holoenzyme substrate recognition, regulation and role in cytokinesis

2017
PMCID: 5586252
PMID: 28884018
DOI: 10.1038/celldisc.2017.27

[…] for controlling cleavage furrow progression and cytokinesis []., all the examples in and are further confirmed to be located in the disordered region based on secondary structural analysis using xtalpred (). these results suggest that pp2a-b′ holoenzymes are recruited by diverse centrosomal and midbody proteins, which might be highly responsive and enhanced by robust mitotic phosphorylation, […]

library_books

BspK, a Serine Protease from the Predatory Bacterium Bdellovibrio bacteriovorus with Utility for Analysis of Therapeutic Antibodies

2017
Appl Environ Microbiol
PMCID: 5288813
PMID: 27940543
DOI: 10.1128/AEM.03037-16

[…] peptidase domain, comprising c99 to i245 (e value, 3.88e−17), as well as a likely signal peptide domain (amino acids 1 to 15). there are no additional conserved domains in the protein sequence. an xtalpred analysis of bspk revealed a predominantly helix-shaped n terminus, with the main part of the protein being structured in β-strands and a few regions of disorder (see fig. s1 […]

library_books

Guidelines for the successful generation of protein–ligand complex crystals

2017
Acta Crystallogr D Struct Biol
PMCID: 5297911
PMID: 28177304
DOI: 10.1107/S2059798316020271

[…] for example, the data generated by structural genomics efforts on all of the protein constructs tested versus successful constructs were used to inform machine-learning approaches as implemented in xtalpred-rf (jahandideh et al., 2014) for scoring different protein constructs., one should keep in mind that the methods used for these predictions bear some degree of uncertainty, and the design […]

library_books

Is unphosphorylated Rex, as multifunctional protein of HTLV 1, a fully intrinsically disordered protein? An in silico study

2016
PMCID: 5613702
PMID: 28955936
DOI: 10.1016/j.bbrep.2016.07.018

[…] of disorder is present in rex protein , , , ., either fully or partially disorder proteins have little tendency to crystallization. therefore, probability of rex crystallization was checked by using xtalpred server (http://ffas.burnham.org/xtalpred-cgi/xtal.pl) , , , . “crystallization feasibility” is a single score that illustrate strongly correlation between several protein properties; […]

library_books

Ca Dependent Folding of Human Calumenin

2016
PLoS One
PMCID: 4798761
PMID: 26991433
DOI: 10.1371/journal.pone.0151547

[…] of the protein was reconstructed using dammif [] and 24 of these calculations were averaged with damaver [] to provide the final envelope., secondary structure prediction was obtained through the xtalpred server []., manual alignment of the ef-hand domains was performed according to rogstam et. al []., three dimensional structure prediction was performed by submitting the amino acid sequence […]


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XtalPred institution(s)
Joint Center for Structural Genomics, La Jolla, CA, USA; BioInfoBank Institute, Poznan, Poland
XtalPred funding source(s)
This server is supported by the NIH Protein Structure Initiative grant U54 GM074898 (JCSG) and NIGMS R01 grant GM095847 'Engineering of Proteins for Crystallography'.

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