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The SBASE domain sequence library, release 10: domain architecture prediction

K. Vlahovicek
2003 Nucleic Acids Research  
The 10th 'jubilee release' of the SBASE library of protein domain sequences contains 1 052 904 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered  ...  SBASE (http://www.icgeb.trieste.it/sbase) is an on-line collection of protein domain sequences and related computational tools designed to facilitate detection of domain homologies based on simple database  ...  ACKNOWLEDGEMENTS The SBASE is established 1990 and is maintained collaboratively by ICGEB, Trieste and the Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.  ... 
doi:10.1093/nar/gkg098 pmid:12520034 pmcid:PMC165545 fatcat:edjcnsfsirhgzbz2qoe6txx2um

The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines

K. Vlahovicek
2004 Nucleic Acids Research  
The present release of the SBASE A library of protein domain sequences contains 972 397 protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into 8547  ...  SBASE (http://www.icgeb.trieste.it/sbase) is an online resource designed to facilitate the detection of domain homologies based on sequence database search.  ...  IMPROVEMENTS WITH RESPECT TO THE PREVIOUS RELEASE DISTRIBUTION AND ACCESS The SBASE domain library browser and domain architecture prediction system are accessible through the web-interface at http:/  ... 
doi:10.1093/nar/gki112 pmid:15608182 pmcid:PMC540066 fatcat:bnrcj4xpzjb7hnhtojc67t3orm

Detecting Atypical Examples of Known Domain Types by Sequence Similarity Searching: The SBASE Domain Library Approach

Somdutta Dhir, Mircea Pacurar, Dino Franklin, Zoltan Gaspari, Attila Kertesz-Farkas, Andras Kocsor, Frank Eisenhaber, Sandor Pongor
2010 Current protein and peptide science  
SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al., Nucl  ...  The current approach uses a curated collection of domain sequences -the SBASE domain library -and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics  ...  ACKNOWLEDGEMENTS The authors are indebted to all previous coworkers who helped the earlier phases of the project, especially to János Murvai for his fundamental role in developing the algorithms and programs  ... 
doi:10.2174/138920310794109148 pmid:20887262 fatcat:p4nfxv7ryreivgd2oysy345k6y

Delineation of modular proteins: Domain boundary prediction from sequence information

L. Kong
2004 Briefings in Bioinformatics  
With the exponential growth of newly determined sequences, our ability to predict domain boundaries rapidly and accurately from sequence information alone is both essential and critical from the viewpoint  ...  The delineation of domain boundaries of a given sequence in the absence of known 3D structures or detectable sequence homology to known domains benefits many areas in protein science, such as protein engineering  ...  L.K. gratefully acknowledges the National University of Singapore for the award of an Agency for Science, Technology and Research, Singapore (A*STAR) scholarship.  ... 
doi:10.1093/bib/5.2.179 pmid:15260897 fatcat:fds3smsmuvewvkndrs5ahaaumu

Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks

J. Murvai
2001 Genome Research  
Applications to the prediction of function are discussed.  ...  An artificial neural network (ANN) solution is described for the recognition of domains in protein sequences.  ...  The SBASE domain sequence library is maintained collaboratively by ICGEB and the Agricultural Biotechnology Center, Gödöllö, Hungary. The advice of Drs. Eugene V.  ... 
doi:10.1101/gr.168701 pmid:11483582 pmcid:PMC311121 fatcat:ale2mgjvunf7xchnt4vru6aelu

SMART: identification and annotation of domains from signalling and extracellular protein sequences

C. P. Ponting, J. Schultz, F. Milpetz, P. Bork
1999 Nucleic Acids Research  
SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/ SMART ).  ...  The tool compares query sequences with its databases of domain sequences and multiple alignments whilst concurrently identifying compositionally biased regions such as signal peptide, transmembrane and  ...  Eisenhaber for helping in linking predicted localisation information and Y. P. Yuan for system administration support.  ... 
doi:10.1093/nar/27.1.229 pmid:9847187 pmcid:PMC148142 fatcat:rkuuub3kubebhaumcbje5wkp2m

In Silico Cloning of Novel Endothelial-Specific Genes

L. Huminiecki
2000 Genome Research  
libraries.  ...  The UniGene gene index was screened using high stringency BLAST against a pool of endothelial expressed sequence tags (ESTs) and a pool of nonendothelial ESTs constructed from cell-type-specific dbEST  ...  In addition, BLAST SBASE (protein domain database at Human Genome Project Resource Centre) suggested a region of similarity to the domain of the intracellular neural cell adhesion molecule long domain  ... 
doi:10.1101/gr.150700 pmid:11076864 pmcid:PMC310981 fatcat:fp3zweppk5d3tdhdyqj4fh7btu

State-of-the-art bioinformatics protein structure prediction tools (Review)

Ioannis Michalopoulos
2011 International Journal of Molecular Medicine  
To deal with the overwhelming data, a collection of automated methods as bioinformatics tools which determine the structure of a protein from its amino acid sequence have emerged.  ...  The aim of this paper is to provide the experimental biologists with a set of cutting-edge, carefully evaluated, user-friendly computational tools for protein structure prediction that would be helpful  ...  If the sequence identity drops below 10% ('midnight zone') (141), then ab initio structure prediction should be employed.  ... 
doi:10.3892/ijmm.2011.705 pmid:21617841 fatcat:46fihfegljgwzccoeerdt2uh64

PRINTS--a database of protein motif fingerprints

T K Attwood, M E Beck, A J Bleasby, D J Parry-Smith
1994 Nucleic Acids Research  
sequence database).  ...  The growth of the databaseis influenced by a number of factors; e.g. the use of multiple motifs; the maximisation of sequence information through iterative database scanning; and the fact that the database  ...  The project benefits from use of the DRAL SEQNET facility.  ... 
pmid:7937065 pmcid:PMC308327 fatcat:kv46fbir2fbo3ngtj2hngtoyvi

Motif identification neural design for rapid and sensitive protein family search

Cathy H. Wu, Sheng Zhao, Hsi-Lien Chen, Chin-Ju Lo, Jerry McLarty
1996 Bioinformatics  
The accelerated growth of the molecular sequencing data has generated a pressing need for advanced sequence annotation tools.  ...  The method has the potential to become a full-scale database search and sequence analysis tool.  ...  Acknowledgment This study is supported in part by grant number R29 LM05524 from the National Library of Medicine, and by the University Research and Development Grant Program of the Cray Research, Inc.  ... 
doi:10.1093/bioinformatics/12.2.109 fatcat:f7qwtvno75b2hknsleprudrf5a

Macromolecular Databases – A Background of Bioinformatics

Tibor Toth, Donatella Verbanac, Dubravko Jelić
2003 Food Technology and Biotechnology  
We would like to express our gratitude to the editors of databases for their courtesy and permission to introduce the database logos, pictures, tables and diagrams within this paper.  ...  SBASE (http:/ /hydra.icgeb.trieste.it/~kristian/SBASE/) SBASE is a library of protein domains and sequences collected from the literature, from protein sequence databases and from genomic databases.  ...  domain architectures.  ... 
doaj:bbe088d5f4874cb4a5ec2c7432482957 fatcat:dia4wh55inb2dgfp37zco5eg5i

XFINGER: A tool for searching and visualising protein fingerprints and patterns

D.N. Perkins, T.K. Attwood
1996 Bioinformatics  
The program runs on Silicon Graphics machines using GL graphics libraries and on machines with X servers supporting the PEX extension: its use is illustrated here by depicting the location of low-density  ...  We have developed a facility to do this: the system allows query sequences to be scanned against either PROSITE, the full PRINTS database, or against individual fingerprints.  ...  This work benefits from the use of the DRAL SEQNET facility.  ... 
doi:10.1093/bioinformatics/12.2.89 fatcat:f2d26txuq5hexofwjol6kkkxwu

A Survey of Computational Methods for Protein Function Prediction [chapter]

Amarda Shehu, Daniel Barbará, Kevin Molloy
2016 Big Data Analytics in Genomics  
Current methods predict function from a protein's sequence, often in the context of evolutionary relationships, from a protein's three-dimensional structure or specific patterns in the structure, from  ...  The latter are related to the different sources of data exploited to predict function, as well as different choices in representing and integrating heterogeneous data.  ...  A machine learning approach is proposed in [48] , where domains extracted from the SBASE library of protein domains [359] are employed as attributes.  ... 
doi:10.1007/978-3-319-41279-5_7 fatcat:pejwmwpoarhyjhulevmkbavocm

Prediction of protein function from protein sequence and structure

James C. Whisstock, Arthur M. Lesk
2003 Quarterly Reviews of Biophysics (print)  
In this article we review the state of the art in function prediction and describe some of the underlying difficulties and successes.  ...  Nevertheless, prediction of protein function from sequence and structure is a difficult problem, because homologous proteins often have different functions.  ...  Lipocalins include the homologues retinol-binding protein with an 8-stranded b-barrel, and retinoic acid-binding protein with a 10-stranded b-barrel. (4) Changing the topology while maintaining the architecture  ... 
doi:10.1017/s0033583503003901 pmid:15029827 fatcat:e3x65am2tvbkdfhcv6d5v5i3je

Cloning and Sequence Analysis of Genes Coding forParameciumSecretory Granule (Trichocyst) Proteins

Marie-Christine Gautier, Linda Sperling, Luisa Madeddu
1996 Journal of Biological Chemistry  
The deduced protein sequences indicate that each precursor gives rise to two of the mature polypeptides found in the crystalline trichocyst matrix.  ...  We present here the first complete sequences of three genes coding for three different precursors of the trichocyst crystalline matrix proteins.  ...  Parry for his kind advice on analysis of heptad repeats and for pointing out to us the likelihood that TMPs contain 4 ␣-helical bundle motifs.  ... 
doi:10.1074/jbc.271.17.10247 pmid:8626591 fatcat:dvytp3n4wvflxlnjy746hvousi
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