LOC3D: annotate sub-cellular localization for protein structures.

Rajesh Nair; Burkhard Rost

doi:10.1093/nar/gkg514

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LOC3D: annotate sub-cellular localization for protein structures.

Rajesh Nair·Burkhard Rost

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Abstract

LOC3D (http://cubic.bioc.columbia.edu/db/LOC3d/) is both a weekly-updated database and a web server for predictions of sub-cellular localization for eukaryotic proteins of known three-dimensional (3D) structure. Localization is predicted using four different methods: (i) PredictNLS, prediction of nuclear proteins through nuclear localization signals; (ii) LOChom, inferring localization through sequence homology; (iii) LOCkey, inferring localization through automatic text analysis of SWISS-PROT keywords; and (iv) LOC3Dini, ab initio prediction through a system of neural networks and vector support machines. The final prediction is based on the method that predicts localization with the highest confidence. The LOC3D database currently contains predictions for >8700 eukaryotic protein chains taken from the Protein Data Bank (PDB). The web server can be used to predict sub-cellular localization for proteins for which only a predicted structure is available from threading servers. This makes the resource of particular interest to structural genomics initiatives.

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Animals Databases, Protein Eukaryotic Cells Internet Neural Networks, Computer Nuclear Localization Signals Protein Conformation Proteins Sequence Analysis, Protein Sequence Homology, Amino Acid User-Computer Interface Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Rajesh Nair, Burkhard Rost. 2003-07-01. LOC3D: annotate sub-cellular localization for protein structures.. https://doi.org/10.1093/nar%2Fgkg514

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