SPAM: Links

Resource	Description
Bayesian Network Model for Protein Fold Prediction	A novel implementation of a Bayesian network which simultaneously learns amino acid sequence, secondary structure and residue accessibility for proteins of known three-dimensional structure.
Bayesian Segmental Models for Protein Secondary Structure Prediction	Web-based secondary structure prediction Server using Bayesian Segmental Models.
The Encyclopedia of Life Project (EOL)	A global collaborative effort to create an electronic reference system for all proteomes. The current focus is to provide an integrated view of structure and functional assignment for all proteins, aka, the volume of Proteins.
Flexible structure AlignmenT by Chaining Aligned fragment paris allowing Twists (FATCAT)	Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists is an approach for flexible protein structure comparison.
Fragnostic	A tool for exploring structure-based connections between proteins which have different folds.
Molecular Biology Toolkit (MBT)	A Java-based protein visualization and analysis toolkit.
Protein Domains	A comprehensive evaluation of protein structural domain assignments.
Proteins of Arabidopsis thaliana (PAT)	A Comparative Proteomics Resource built for the proteins of Arabidopsis thaliana.
Structural Protein Domain Classification	A database for automated classification of DNA-binding domains in PDB, as well as Gene Ontology assignment for PDB chains.
Segment Alignment Server (SEA)	Protein pairwise alignment using predicted local structure segments to describe proteins and network matching algorithm.
Contact Map Prediction Server	Web-based contact map prediction server using Bayesian Segmental Models.
Contributions to the PDB structural Genomics Web Site	Functional annotation by structure, structural genomics targets and homology models relative to known functional annotation of the human genome.
Disease Modelling	Modelling of diease related protein and complexes .
Genome strUcture Target Selection System (GUTSS)	Provides the user with an initial interface designed to help set physico-chemical criteria compatible with protein crystallizability, and for locating those with biological interest and without structural homologs.
Partial Order Structure Alignment (POSA)	Multiple flexible structure alignment using partial order graphs.
Joined Assembly of Function Annotations (JAFA)	None
Topological Protein Structure Alignment (TOPOLOG)	Structure alignment based on local geometric properties
CE - Protein Structure Alignment by Cominatorial Extension Algorithm	Protein structures pairwise alignment. Search against the representative set of PDB protein structures. Download CE software or precalculated alignments.

Shading indicates funding is solely by SPAM

The SPAM project is supported by the National Institutes of Heath (NIH) grant number GM63208 and is located within the Skaggs School of Pharmacy and Pharmaceutical Sciences and the San Diego Supercomputer Center (SDSC) at the University of California San Diego (UCSD), the Keck Graduate Institute (KGI) and the Burnham Institute (TBI).

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