Protein Resources

GELLAB-II 2D Gel Analysis  
GELLAB-II is an integrated collection of programs for the analysis of 2D electrophoretic gels. Currently, it runs on UNIX systems. The display of gel images is available if the hardware supports a color display under X-windows. These programs were developed at the Image Processing Section in the National Cancer Institute.
Submitted: Dec 03, 2000
NCI Flicker  
Flicker is a method for comparing images from different Internet sources on your Web browser. The Flicker image viewer is a Java applet which reads two images from the Internet and then displays them in the your Web browser. It allows you to enhance them in various ways and to compare them visually in a third window called the flicker window.
Submitted: Dec 03, 2000
Carbohydrate-Active Enzymes  
This server describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Submitted: Dec 02, 2000
3D ALI  
A database of aligned protein structures and related sequences.
Submitted: Jan 05, 2001
Phosphoprotein Database (PPDB)  
The purpose of a Phosphoprotein Database (PPDB) is to promote a systematic approach to the study of cellular protein phosphorylation. PPDBs have the potential to transform 2DE images from mere collections of spots on gels into images that convey information about cell lineage, the activation state of the cell, the ligands that the cell has encountered, the kinases, phosphatases and substrates present in the cell, and the activation state of these enzymes.
Submitted: Dec 03, 2000
2-DE Database for Human Heart Proteins  
This is the two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database for human heart proteins. It contains data on proteins identified on the 2-D PAGE maps of ventricle and atrium of human heart.
Submitted: Dec 03, 2000
EF-Hand Calcium-Binding Proteins Data Library  
Information about the EF-hand calcium-binding protein family, including sequence, structure, and function data.
Submitted: Nov 25, 2000
Lipase Engineering Database  
This Internet database provides information on sequence and structure of lipases to facilitate protein engineering. We acknowledge your comments or contribution to this page: please send us information to be included in this database.
Submitted: Dec 02, 2000
Parasite host cell interaction 2D-PAGE database at the Department of Medical Microbiology and Immunology of the University of Aarhus.
Submitted: Dec 03, 2000
PSA Structure Prediction  
The Protein Sequence Analysis (PSA) server predicts protein secondary and tertiary structure based on sequence, and is available for researchers who have amino acid sequences for proteins of unknown structure and for which no homologous sequences are known. To use PSA, one submits a single amino acid sequence to the server, which may be instructed to analyze the sequence in one of three ways: using Type-1, Type-2, or WD-repeat DSMs. DSMs are Discrete State-space Models for patterns of alpha-helices, strands, tight turns, and loops in specific structural classes.
Submitted: Dec 02, 2000
SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE reference maps. You can locate these proteins on the 2-D PAGE maps or display the region of a 2-D PAGE map where one might expect to find a protein from SWISS-PROT.
Submitted: Dec 03, 2000
The Protein Structure Database (PSdb)  
The Protein Structure Database (PSdb), is a protein database, dervived from the information available in the Protein Databank and NRL-3D database, that relates secondary (e.g. Helix, Sheet, Turn, Random Coil) and tertiary information (e.g. Solvent accessibility, internal relative distances, and ligand interactions) to the primary structure.
Submitted: Dec 02, 2000
A Protein Quaternary Structure File Server  
The Protein Quaternary Structure file server ( PQS ) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank (PDB) that were determined by X-ray crystallography.
Submitted: Oct 19, 2000
Chromatin Structure & Function Page  
This site is intended to disseminate information regarding the rapidly evolving and highly exciting field of chromatin structure, proteins that modify chromatin structure, and the effects that these modifications have on cell function.
Submitted: Dec 02, 2000
The CPHmodels World Wide Web server predict protein structure using comparative (homology) modelling.
Submitted: Dec 09, 2000
FYVE Finger  
The FYVE finger is a novel zinc finger-like domain found in several proteins involved in membrane trafficing. The basic motif consists of 8 Cysteins, 4 of which are part of the core motif R+HHC+XCG (where '+' is a positively charged residue and 'X' is any aminoacid). This finger has only been observed as a single copy in each of the proteins and it has been shown to bind 2 zinc ions per finger. In this work, it was shown that the EEA1 (Early Endosome Associated protein 1) requires it's FYVE finger for endosomal localisation, - and most likely, the EEA1 FYVE finger is sufficient for endosome targeting of this protein. The FYVE fingers in other proteins may play similar roles.
Submitted: Dec 02, 2000
High-Performance Heart  
Heart High-Performance 2-DE Database contains about 3300 proteins of ventricle resolved by large gels (23 cm x 30 cm x 0.075 cm). Proteins were detected by silver staining. 2-DE patterns were evaluated by the TopSpot software package.
Submitted: Dec 03, 2000
Joint Protein Structure Laboratory  
Homepage of JPSL, Joint Protein Structure Laboratory, Ludwig Institute for Cancer Research and The Walter and Eliza Hall Institute of Medical Research. Proteomic databases, techniques and methods, staff, publications and news and conferences.
Submitted: Dec 03, 2000
The Make2ddb package lets you easily create a 2-DE database on your Web server, with search functions, such as by accession number, by description, by author, and by clicking on a spot, similar to SWISS-2DPAGE.
Submitted: Dec 03, 2000
Module Pages  
The module pages contain information and research tools on mobile protein domains, developed, collected and maintained by the Bork group and various collaborators.
Submitted: Dec 02, 2000
NIMH-NCI Protein-Disease Database  
This server is part of the NIMH-NCI Protein-Disease Database project for correlating diseases with proteins observable in serum, CSF, urine and other common human body fluids based on biomedical literature.
Submitted: Dec 03, 2000
Protein Information Resource  
The Protein Information Resource (PIR), in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a comprehensive, annotated, and non-redundant protein sequence database in which entries are classified into family groups and alignments of each group are available.
Submitted: Sep 27, 2000
Protein Kinase Resource  
The Protein Kinase Resource (PKR) is a web accessible compendium of information on the protein kinase family of enzymes. This resource includes tools for structural and computational analyses as well as links to related information maintained by others. The PKR is a collaborative project of protein kinase researchers and computational biologists working to create a database integrating molecular and cellular information.
Submitted: Nov 23, 2000
Protein Mutant Database  
The Protein Mutant Database (PMD) covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants.
Submitted: Sep 19, 2000
Protein Spotlight  
Protein Spotlight (ISSN 1424-4721) is a periodical electronic review from the SWISS-PROT group of the Swiss Institute of Bioinformatics (SIB). It is published on a monthly basis and consists of articles focused on particular proteins of interest. Each issue is available, free of charge, in HTML or PDF format.
Submitted: Dec 02, 2000
ProteoMetrics, LLC is a bioinformatics company that develops innovative software to rapidly identify and characterize proteins. The company developed out of an academic effort to more effectively utilize proteomic research and has now expanded into the commercial sector. Currently, a major focus of its activity is the development of an advanced intranet framework to support large-scale, high-throughput proteomics projects.
Submitted: Dec 02, 2000
SANT Domain  
SANT domains are a epeated motif in N-CoR, the nuclear receptor co-repressor.
Submitted: Dec 02, 2000
Two-dimensional polyacrylamide gel electrophoresis database. You can search in SIENA-2DPAGE by description line (DE) or by ident (ID), by accession number (AC line), by clicking on a spot: select one of the reference maps, click on a spot and then get the corresponding information from the database, by author (RA lines), or get a list all entries.
Submitted: Dec 03, 2000
Simon's Guide  
This web site is a database for the Eph family of receptor protein tyrosine kinases and their ligands, the ephrins. Much excitement regarding this new family results from their roles in developmental neurobiology as molecular guides for axons. However, they may be involved in many other processes; cancer, angiogenesis, haematopoiesis, and kidney development. The expression patterns of members in this family suggest that their functions during development and in the adult organism is still relatively unknown. It is salient that their name derives from the initial cloning, by Hirai in 1987, of the Eph receptor from an erythropoietin (hormone for the production of red blood cells) producing hepatocellular carcinoma cell line, which illustrates their potential importance in many systems.
Submitted: Dec 02, 2000
The RCSB Protein Data Bank  
The single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
Submitted: Sep 15, 2000
The RNase P Database  
The RNase P Database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information.
Submitted: Dec 02, 2000
TMbase is a database of transmembrane proteins and their helical membrane- spanning domains. TMbase was originally meant as a tool for analyzing the properties of transmembrane proteins.
Submitted: Dec 02, 2000
Yeast Protein Map from Bordeaux  
2D Gel Map of Saccharomyces cerevisiae proteins.
Submitted: Dec 03, 2000

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