Functional Protein Sequence Pattern Database

Ricardo Núñez Miguel
The Functional Protein Sequence Pattern Database (FPSPD) is a fully automated database of protein sequences patterns derived from the analysis of the conserved residues that are predicted to be functional in structurally-aligned homologous families in the HOMSTRAD database.The functional patterns predicted by FPSPD are those that include residues that are directly involved in functional interactions with co-factors, substrates, intermediates, products, and other proteins.

Different methods have been used in the developtment of FPSPD. Environment-dependent substitution tables and evolutionary trace analysis to identify those residues that can be considered involved in functional interactions. Solvent accessibility calculations to estimate the availability of particular residues and patterns to be directly involved in functional interactions. And, finally, knowledge of the three-dimensional structure to estimate the borders of the patterns.

The method yielded 3584 patterns, from 617 HOMSTRAD families, that are considered functional and 3049 that are probably functional. FPSPD Could be useful for assigning a protein to a homologous superfamily and thereby providing clues about function.


Structural validation by assessment of the Ramachandran plot

Paul de Bakker and Simon Lovell
RAMPAGE is a program for visualising and assessing the Ramachandran plot of a protein structure. On the basis of a manually curated set of high-quality protein structures (from the Richardson's Group at Duke University) and a number of filters (such as B-factor cutoff and van der Waals clashes), reference phi/psi plots were derived for Gly, Pro, pre-Pro and general (other) residue types, and subdivided into "favoured", "allowed" and "outlier" regions. Residues in the uploaded PDB file that fall into the "allowed" and "outlier" regions are listed, and a picture of the Ramachandran plot is displayed. The output can also be printed as a high-resolution multi-colour Adobe PDF or PostScript file, containing the general plot and the four separate plots (2 pages). A corresponding Kinemage file can be downloaded or inspected using the interactive JavaMage applet.


A fold recognition method using structural environment-specific substitution tables and structure-dependent gap penalties

Jiye Shi, Tom L. Blundell, Kenji Mizugichi
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.

TraceSuite II

A fully automated evolutionary trace server

Jiye Shi, Axel Innis, Lan Chen and Tom L. Blundell
TraceSuite II is a fully automated evolutionary trace (ET) server. The main purpose of this server is to speed up the ET analysis by providing the users with both easy-to-use interface and easy-to-interperate output with (hopefully) nice graphics.

The server takes a sequence alignment as the input and performs ET analysis. The resulting phylogenetic tree and the trace information are available in both JPEG and PostScript format. Any sequences with a PDB code as the sequence name will be regarded as known structures and the server will retrieve the PDB co-ordinates files and map the ET results onto each structure. Rasmol and Molscript input files for the mapping are provided for viewing and/or high-resolution printing.


Protein structure and alignment analysis

Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington
JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. The JOY representation constitutes an essential part of the two databases of protein structure alignments: HOMSTRAD and CAMPASS. It is also used for identifying distant homology by the program FUGUE.

JOY takes an input alignment (or a single sequence) in a format similar to that of the NBRF/PIR format and produces a number of output files, including the annotated alignment in PostScript, LATEX and HTML. JOY requires a series of datafiles containing information about secondary structures, solvent accessibility and hydrogen bonding. These are produced automatically from a PDB file


Site Directed Mutator for predicting stability changes upon mutation

Catherine L. Worth, Tom L. Blundell, Chris M. Topham and N. Srinivasan.
SDM can be used to assess the impact that a nsSNP will have on protein stability by calculating a stability score. SDM requires as input a wild-type structure and a mutant structure - the latter can be generated by our program Andante.


Systematic Annotation of Marcro molecULes

Sung Gong

SAMUL is a web-based database system in which users can browse structural and functional annotations proteins at their residue level. The local structural environment (by the scheme of 64 environments) of amino acid residues can be determined by JOY and visualized in the context of three-dimensional structure with Jmol, a molecular viewer. For functional annotations, 26 UniProt feature annotations are utilized and the information is transferred onto their corresponding positions in terms of three-dimensional structures if available.

SAMUL also accommodates amino acid variations and mutations information so that users could browse and interprete them by looking their structural and functional environments at the same time.