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LOC3D: annotate sub-cellular localization for protein structures

R. Nair
2003 Nucleic Acids Research  
The web server can be used to predict sub-cellular localization for proteins for which only a predicted structure is available from threading servers.  ...  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)  ...  ACKNOWLEDGEMENTS We are grateful to Jinfeng Liu and Megan Restuccia (Columbia) for computer assistance and Kaz (Columbia) for valuable discussions.  ... 
doi:10.1093/nar/gkg514 pmid:12824321 pmcid:PMC168921 fatcat:tzrv267iaffinb2cpckvofi3w4

LOCnet and LOCtarget: sub-cellular localization for structural genomics targets

R. Nair, B. Rost
2004 Nucleic Acids Research  
LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular  ...  The web server can be used to predict sub-cellular localization of proteins from their amino acid sequence.  ...  ACKNOWLEDGEMENTS Thanks to Jinfeng Liu and Megan Restuccia (Columbia) for computer assistance and to Kaz Wrzeszczynski (Columbia) for valuable discussions.  ... 
doi:10.1093/nar/gkh441 pmid:15215440 pmcid:PMC441579 fatcat:77gxe5nz4fgsljdohhtfpo4ery

Better prediction of sub-cellular localization by combining evolutionary and structural information

Rajesh Nair, Burkhard Rost
2003 Proteins: Structure, Function, and Bioinformatics  
The native sub-cellular compartment of a protein is one aspect of its function. Thus, predicting localization is an important step toward predicting function.  ...  We therefore developed two separate systems: one for proteins of known structure and one for proteins of unknown structure.  ...  Predicting the localizations for all eukaryotic proteins in PDB. Finally, we annotated sub-cellular localization for all eukaryotic protein chains in PDB.  ... 
doi:10.1002/prot.10507 pmid:14635133 fatcat:vhwfh7izzram5ppsbu545fkiky

Annotating proteins from endoplasmic reticulum and Golgi apparatus in eukaryotic proteomes

K. O. Wrzeszczynski, B. Rost
2004 Cellular and Molecular Life Sciences (CMLS)  
Nucleic Acids Res. 31: 397—399 Nair R. and Rost B. (2003) Loc3d: annotate sub-cellular local- ization for protein structures.  ...  Conclusions Annotating sub-cellular localization is an essential aspect of large-scale experimental endeavors.  ... 
doi:10.1007/s00018-004-4005-3 pmid:15170512 fatcat:pmwllv6n2rgshff7h43d4nvkga

Bird Eye View of Protein Subcellular Localization Prediction

Ravindra Kumar, Sandeep Kumar Dhanda
2020 Life  
We hope the review will be useful for the researchers working in the field of protein localization predictions.  ...  In addition, it is essential for proteins to be destined to their specific locations or compartments to perform their structure and functions.  ...  We gratefully acknowledge Rajrani Ruhel for critically reading the manuscript. No funding is received to write and compile this review article.  ... 
doi:10.3390/life10120347 pmid:33327400 pmcid:PMC7764902 fatcat:4kfiezcrlfh4vmjh6bh5ysgwty

Annotating Protein Function through Lexical Analysis

Rajesh Nair, Burkhard Rost
2004 The AI Magazine  
sub-cellular localizations is found. All exact Semiautomated methods are based on build- matches of each of the subvectors to any of the ing dictionaries of rules.  ...  Sequence Conserved for lem. Current Opinion in Structural Biology 7(1): 53–59. Subcellular Localization. Protein Science 11(12): Hatzivassiloglou, V.; Duboue, P.  ... 
doi:10.1609/aimag.v25i1.1746 dblp:journals/aim/NairR04 fatcat:eoinvyqphjg4zmk2jvyoiukpfa

Computational Analysis of Modular Protein Architectures [chapter]

Rune Linding, Ivica Letunic, Toby J. Gibson, Peer Bork
2005 Modular Protein Domains  
Thanks to Kresten Lindorff-Larsen, Sophie Chabanis-Davidson, Sara Quirk, and Francesca Diella for commenting on this chapter. Thanks to Pål Puntervoll and Manuela Helmer Citterich for figures.  ...  Detecting nonenzymatic regulatory domains is essential to predicting a protein's cellular role, binding partners, and subcellular localization.  ...  Below, we discuss how to annotate and analyze protein sequences for modular domains and linear motifs.  ... 
doi:10.1002/3527603611.ch21 fatcat:3oar56fhrnasrgfc35dfutok4m

Implicit motif distribution based hybrid computational kernel for sequence classification

V. Atalay, R. Cetin-Atalay
2004 Bioinformatics  
P2SL additionally offers the distribution potential of proteins among localization classes, which is particularly important for proteins, shuttle between nucleus and cytosol.  ...  P2SL hybrid computational system achieved ∼81% of prediction accuracy rate over ER targeted, cytosolic, mitochondrial and nuclear protein localization classes.  ...  Ozturk (Bilkent University, Turkey) for his critical discussions on this paper and M. Ozarar for the initial technical assistance. This work was supported by the Turkish Academy of Sciences to R.C.A.  ... 
doi:10.1093/bioinformatics/bti212 pmid:15598837 fatcat:7khtollt3ndy5ohfpkvcp26rgi