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Associated diseases

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AnnoLyze specifications

Information


Unique identifier OMICS_26616
Name AnnoLyze
Interface Web user interface
Restrictions to use None
Input data A chain code and thresholds for filtering sequence and structure similarities.
Input format PDB
Output data An automatic annotation of the protein structures.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Marc A. Marti-Renom <>

Publications for AnnoLyze

AnnoLyze in publications

 (4)
PMCID: 4671658
PMID: 26642067
DOI: 10.1371/journal.pone.0142293

[…] and targets was built to identify the most likely targets of a given compound in the gsk dataset. to explore the structural space, we used nannolyze, an improved version of our previously published annolyze algorithm [], which was based on homology detection through structural superimposition of targets and their interaction networks to small compounds, similar to previously published […]

PMCID: 3789770
PMID: 24098102
DOI: 10.1371/journal.pcbi.1003253

[…] the identification of likely targets based on the structural similarity of compounds and protein targets with known three-dimensional structures. the method was based on an improved version of the annolyze program . finally, the exploration of the historical data on screening assays resulted in testable hypotheses for the anti-mycobacterium mode of action of the selected compounds, based […]

PMCID: 2667270
PMID: 19381286
DOI: 10.1371/journal.pntd.0000418

[…] models as well as predicted locations of binding sites for small molecules on their surfaces and predicted types of molecules they bind. the pipeline, which relies on the modpipe package and the annolyze program , has been applied to genomes of ten pathogens that cause tropical diseases. the output of the pipeline has been stored in a relational database for easy searching and dissemination […]

PMCID: 1892079
PMID: 17570143
DOI: 10.1186/1471-2105-8-S4-S1

[…] from 0 to 13.6%, mostly reflecting the inability of sequence similarity search procedures to detect substrate specificity., marti-renom and colleagues [] introduce two new programs, annolite and annolyze, which add functional content to the previously established dbali database of protein structure alignments []. the annolite program utilizes structural alignments to transfer functional […]


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AnnoLyze institution(s)
Structural Genomics Unit, University of California at San Francisco, San Francisco, CA, USA; Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA; California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA, USA; Functional Genomics Unit, Bioinformatics Department, Centro de Investigacion Principe Felipe (CIPF), Valencia, Spain
AnnoLyze funding source(s)
Supported by The Sandler Family Supporting Foundation, NIH grants GM 62529, GM074929, GM71790 and GM54762.

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