Structure Alignment

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Optimal Global Alignment of Two Sequences with No Short-cuts at
and Align at MIPS, Germany 

Evaluates the quality of a protein structure by Roman Laskowski, 
University College, London

*2*PROVE :-
Analysis of Protein Atomic Volumes at UCMB, Belgium

A versatile structure analysis program for mutant prediction,
structure verification, molecular graphics and more
by Gert Vriend, EMBL, Germany


*3*3D-ALI :-

Database relating Proteins Structures and Sequences
 at  EMBL-Heidelberg

*2*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 :
under directory /pub/software/unix,
file clustering.tar.Z
-ASC  :-
Analytic Surface Calculation of PDB Protein Structures at

-GRASP  :-
Display and manipulation of molecular surfaces, coloured to represent
electrostatic and other properties by Anthony Nicholls, Columbia
University, USA

Model building from an amino acid sequence and the structures of
known, related proteins,  a module of InsightII, from MSI,
incorporating Greer's principles

*2*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

Analyses PDB data for secondary structure including turns by
Gail Hutchinson, University College, London

*3*Sleuth :-
Amino Acid Conformation and Solvent Accessibility of
PDB Files at Washington U. FTP

*2*STRIDE :-
Find Secondary Structural Elements in PDB Proteins Structures
at EMBL-Heidelberg

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

*3*Motif-based searching in TOPS protein topology databases


X ray and NMR structure refinement package

a collection of disparate programs covering most of the computations required
for macromolecular crystallograp

A molecular replacement package