Structure Alignment

ALIGN:-

Optimal Global Alignment of Two Sequences with No Short-cuts at

http://www.biochem.ucl.ac.uk/bsm/dbbrowser/ALIGN/ALIGN.html

and Align at MIPS, Germany

PROCHECK :-

Evaluates the quality of a protein structure by Roman Laskowski,

University College, London

PROVE :-

Analysis of Protein Atomic Volumes at UCMB, Belgium

WHAT IF :-

A versatile structure analysis program for mutant prediction,

structure verification, molecular graphics and more

by Gert Vriend, EMBL, Germany

3D-ALI :-

Database relating Proteins Structures and Sequences

at EMBL-Heidelberg

Automated analysis of interatomic contacts in proteins

LPC - ligand-protein contacts

CSU - contacts of structural units

Clustering of non-polar contacts in proteins

Available on request from the author

FlexX :-

Docking of hydrophobic ligands with interaction-based matching algorithms

Clustering :-

Domain identification by clustering sequence alignments.

This program is available by anonymous ftp at :

ftp.embl-ebi.ac.uk

under directory /pub/software/unix,

file clustering.tar.Z

ASC :-

Analytic Surface Calculation of PDB Protein Structures at

EMBL-Heidelberg

GRASP :-

Display and manipulation of molecular surfaces, coloured to represent

electrostatic and other properties by Anthony Nicholls, Columbia

University, USA

HOMOLOGY :-

Model building from an amino acid sequence and the structures of

known, related proteins, a module of InsightII, from MSI,

incorporating Greer's principles

MOOSE :-

Macromolecular Object Oriented Search Engine to Extract PDB Contained

Information at Columbia U.

PKB :-

A Relational Protein Structure Database Tool

A program system for analysis of protein structure, requiring SPlus FTP

PROMOTIF :-

Analyses PDB data for secondary structure including turns by

Gail Hutchinson, University College, London

Sleuth :-

Amino Acid Conformation and Solvent Accessibility of

PDB Files at Washington U. FTP

STRIDE :-

Find Secondary Structural Elements in PDB Proteins Structures

at EMBL-Heidelberg

TOPITS :-

Fold recognition for a single sequence, based on secondary structure

prediction by Rost & Sander, EMBL, Germany

TOPS :-

Creates protein topology cartoons from PDB and DSSP files

by Tom Flores while at the University College, London

Motif-based searching in TOPS protein topology databases

CRYSTALLOGRAPHY PROGRAMS AVAILABLE AT SERC

XPLOR / CNS

X ray and NMR structure refinement package

CCP4

a collection of disparate programs covering most of the computations required

for macromolecular crystallograp

AMORE

A molecular replacement package