Structure Alignment

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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

 
*2*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

 

*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 :
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

 
*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

 
-PROMOTIF :-
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

 
-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


*3*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