Gathering Homologs using Blast and using Flowerpower

DISOPRED - http://bioinf.cs.ucl.ac.uk/disopred/ This server predicts natively disorder regions (encoded in the protein sequence). These disordered regions represent flexible and dynamic regions. Disorder regions can represent molecular recognition of proteins and nucleic acids. “The absence of a static structure means that disordered residues do not appear in the electron density maps obtained by X-ray crystallography but they can be investigated using other types of spectroscopy such as circular dichroism and NMR (…)DISOPRED2 was trained on a set of around 750 non-redundant sequences with high resolution X-ray structures. Disorder was identified with those residues that appear in the sequence records but with coordinates missing from the electron density map. This is an imperfect means for identifying disordered residues as missing co-ordinates can also arise as an artifact of the crystalization process. False assignment of order can also occur as a result of stabilizing interactions by ligands or other macromolecules in the complex. However, this is the simplest means for defining disorder in the absence of further experimental investigation of the protein. A sequence profile was generated for each protein using a PSI-BLAST search against a filtered sequence database. The input vector for each residue was constructed from the profiles of a symmetric window of fifteen positions. The data were used to train linear support vector machines (SVMs). The SVM controls overfitting by ensuring that the decision surface separates the two classes with a large margin. An example linear decision surface that separates two classes in 2D” – from the DISOPRED web-site.

Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT (2004)

Prediction and functional analysis of native disorder in proteins from the three kingdoms of life - Journal of Molecular Biology, 337, 635-645

Microarray Database:

ONCOMINE: http://www.oncomine.org/resources/catalogModule/storeValue.jsp

Transmembrane predictors:

THMM: http://www.cbs.dtu.dk/services/TMHMM/

Phobius: http://phobius.cgb.ki.se/

3-D structure prediction:

PHYRE: This is a new server that that recognizes a fold , the idea is that if there is a protein with solved structure similar to your protein, they can try folding it using the coordinates of the known structure (called threading, their precedent is that the protein sequence folds by itself), this is worth giving it a try. http://www.sbg.bio.ic.ac.uk/phyre/

3d-pssm: This is the previous version of Phyre and is still my favorite http://www.sbg.bio.ic.ac.uk/~3dpssm/index2.html

JNET, a good secondary structure predictor http://www.compbio.dundee.ac.uk/~www-jpred/jnet/

SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.html

MODELLER: http://salilab.org/modeller/modeller.html

http://phylogenomics.berkeley.edu/cgi-bin/homology_model/build_model_data.py

Swiss model:

Predicting Domains:

PHYLOFACTS: Submit your protein to phylofacts and see if there are domains already identified by this server

http://phylogenomics.berkeley.edu/phylofacts/input_phylofacts.php?library=structureprediction

SMART: http://smart.embl-heidelberg.de/

Superfamily: http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

PFAM: Submit your protein to pfam and see if there are domains already identified by this server

http://pfam.wustl.edu/hmmsearch.shtml

SCOP hierarchy, according to SCOP, protein domains in the same SCOP superfamily are believed to be homologous.

Other remote homolog detection algorithms: Target98, Psi-Blast, ISS, Fasta and Blast

Jake Glann Gunville’s handy toolkit

Germ Online - http://www.germonline.org/index.html

“This gives information on the transcript, you can browse the chromososmes, gene locus, … GermOnline is a cross-species knowledgebase that provides classical and tiling microarray data relevant for the cell cycle and gametogenesis. The report page integrates data on DNA sequence, RNA concentration, length and exon composition as well as information on protein function, structure and network interaction.”

Arabidopsis Information Resource - http://www.arabidopsis.org/

“The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information,”

MIPS - http://mips.gsf.de/projects/plants

Database of Interacting Proteins - http://dip.doe-mbi.ucla.edu/

“The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data”

Entrez-Gene - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

Flybase - http://www.flybase.org/

Gene DB - http://www.genedb.org/

Salmonella - http://www.salmonella.org/

EC – PDB THORTON’S GROUP

MIPS

JGI

EC DATABASE

Structure function linkage Database

BPG WIKI

Genomes ONLINE

National Microbial Pathogen Data Resource

Risk Group Classification for Infectious disease web-site

MicrobeWiki:

IntAct Site: IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

HMM tutorial: http://www.soe.ucsc.edu/research/compbio/ismb99.tutorial.html

UCSC bioinformatics website

Sam tutorial

Dali. An electronic mail/WWW server that performs a 3D similarity search in the PDB, given the atomic coordinates of a 3D protein model as input (3). The analog of a BLAST server for 3D structures. http://www2.embl-ebi.ac.uk/dali/

DSSP. A database of secondary structure, solvent accessibility and other information derived from 3D structures in the PDB. http://www.sander.embl-ebi.ac.uk/dssp/ ; personal Email: sander@embl-ebi.ac.uk

GPCRDB. Information system for G-protein coupled receptors. http://swift.embl-heidelberg.de/7tm/ ; personal Email: vriend@embl-heidelberg.de

nrdb90. A non-redundant sequence database that removes sequences at a redundancy level of 90% amino acid identity (15). Weekly updates. http://www.embl-ebi.ac.uk/~holm/nrdb90

PredictProtein. An electronic mail server that provides a predicted secondary structure and solvent accessibility profile for any protein sequence with homologues in Swiss-Prot. Rated at 72% sustained three-state accuracy (16). http://www.embl-heidelberg.de/predictprotein/ ;

__________Process of Go annotation

http://www.geneontology.org/GO.function.guidelines.shtml

amiGO

GO EVIDENCE CODE

Open Biomedical Ontologies is an umbrella web address for well-structured controlled vocabularies for shared use across different biological and medical domains.

Kegg: To downloads data click here: ftp://ftp.genome.jp/pub/kegg/xml/

__________GENOMES:

NCBI Bacterial genomes: ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/

All known genomes: Genomes online

COMPARATIVE GENOMES

http://genolist.pasteur.fr/Leproma/

Model Organism databases:

Model Organism Database/release

COGs

H. sapiens NCBI 36http://www.germonline.org/Homo_sapiens/index.html

M. musculus NCBI m36http://www.germonline.org/Mus_musculus/index.html

R. norvegicus RGSC 3.4

D. rerio Zv 6

D. melanogaster BDGP 4

C. elegans WS 150

A. thaliana TIGR

S. pombe Sanger

S. cerevisiae SGD 1

UC-Extension http://www.unex.berkeley.edu/cat/bio.html#drug