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COLORADO3D specifications

Information


Unique identifier OMICS_33955
Name COLORADO3D
Alternative name COLORADO-3D
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some alignments of multiple sequences.
Input format PDB
Output data A file including values of the chosen parameter: structure quality, residue burial or conservation.
Output format PDB
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Joanna Sasin

Publication for COLORADO3D

COLORADO3D citations

 (14)
call_split

Cellular Effects of Curcumin on Plasmodium falciparum Include Disruption of Microtubules

2013
PLoS One
PMCID: 3591428
PMID: 23505424
DOI: 10.1371/journal.pone.0057302
call_split See protocol

[…] dividual monomers of alpha and beta-tubulin were modeled based on the principle of homology modeling by SWISS-MODEL server . Structures of both the monomers were validated using ANOLEA program in the COLORADO 3D server . The dimeric form of parasite tubulin was constructed by assembling these two monomers using the protein-protein docking server HEX .The crystal structure of curcumin has been publ […]

call_split

Insights into the structure, function and evolution of the radical SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria

2009
Nucleic Acids Res
PMCID: 2836569
PMID: 20007606
DOI: 10.1093/nar/gkp1142
call_split See protocol

[…] with PyMOL (). Mapping of the electrostatic potential on protein surfaces was done with Adaptive Poisson-Boltzmann Solver (APBS) (). Mapping of sequence conservation on protein surfaces was done with COLORADO3D () and CONSURF (). […]

library_books

A novel 9 bp insertion detected in steroid 21 hydroxylase gene (CYP21A2): prediction of its structural and functional implications by computational methods

2009
J Biomed Sci
PMCID: 2653521
PMID: 19272182
DOI: 10.1186/1423-0127-16-3

[…] structural anomalies could thus have been passed down from the template during modeling (see Additional file ). The structures were also colour-rendered based on the Verify3D scores generated by the Colorado3D server. The major part of the structures, in all the cases, had a good score (see Additional file ). […]

call_split

Type II restriction endonuclease R.Hpy188I belongs to the GIY YIG nuclease superfamily, but exhibits an unusual active site

2008
BMC Struct Biol
PMCID: 2630997
PMID: 19014591
DOI: 10.1186/1472-6807-8-48
call_split See protocol

[…] pect to the unknown true structure) was selected as the final model. Mapping of sequence conservation onto the model was done for the multiple sequence alignment of the Hpy188I family, initially with COLORADO3D [], and ultimately with the ConSurf server []. […]

library_books

MetaMQAP: A meta server for the quality assessment of protein models

2008
BMC Bioinformatics
PMCID: 2573893
PMID: 18823532
DOI: 10.1186/1471-2105-9-403

[…] or) fields replaced with the MetaMQAP scores. One option corresponds to linear scaling of values onto the range of 0.00 (predicted no deviation) and 99.99 (predicted deviation ≥ 10 Å), similar to the COLORADO3D server []. If an option of 'absolute values' was used, then raw MetaMQAP scores are reported without scaling (i.e. B-factor contains the predicted absolute per-residue deviations in Å). The […]

call_split

The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK)

2008
Nucleic Acids Res
PMCID: 2425500
PMID: 18420655
DOI: 10.1093/nar/gkn169
call_split See protocol

[…] d using the ROSETTA method () for de novo (template free) protein structure prediction. Model quality has been assessed using PROQ (). Mapping of sequence conservation onto the model was done via the COLORADO3D server (), using the Rate4Site method, with the JTT substitution matrix and ML model for rate inference. […]

Citations

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COLORADO3D institution(s)
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
COLORADO3D funding source(s)
Supported by the Polish State Committee for Scientific Research (grant PBZ-KBN-088/ P04/2003).

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