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.


Swanand Gore, Anjum Karmali, Nick Furnham
RapperTK is a versatile toolkit for conformational sampling under restraints. It is a generalization of RAPPER .


Restraint-based protein modelling

Paul de Bakker, Mark DePristo, Reshma Shetty, Nick Furnham
RAPPER is a discrete conformational sampling algorithm for restraint-based protein modelling. It has been used for all-atom loop modelling, whole protein modelling under limited (C-alpha) restraints, comparative modelling, ab initio structure prediction, structure validation, and experimental structure determination with X-ray and nuclear magnetic resonance spectroscopy.


Voronoi tessellation analysis of macromolecules

Swanand P. Gore, David F. Burke and Tom L. Blundell
It uses Qhull program to calculate tessellations and (optionally) Groamcs to solvate the system. A faster solvation method is also available. Provat brings flexibility and easy visualization to macromolecular tessellation. There are various ways to group atoms and define metasites. There are various datastyles to output the interfaces. A PyMOL plugin provides a convenient way to visualize the output.


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


A new environment-specific substitution table (ESST) generator

Semin Lee, Tom L. Blundell
Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla , a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled using an entropy-based smoothing procedure to estimate robust substitution probabilities.