Structural Bioinformatics 2000

by


f P. C. Lyu & J. K. Hwang

PDB

ExPASY

NCBI

NCSA Biology WorkBench

 


Getting Protein Structures

 

Viewing Protein Structures

 

Using Protein Tools

Multiple Sequence Alignment

 

 Retrieving DNA sequence



 

Prediction of Physical Properties

Compute pI/MW        http://expasy.nhri.org.tw/tools/pi_tool.html

PeptideMass           http://expasy.nhri.org.tw/tools/peptide-mass.html

SAPS                     http://www.isrec.isb-sib.ch/software/SAPS_form.html

Prediction of Protein Identity Based on Composition

AACompIdent          http://expasy.nhri.org.tw/tools/aacomp/

AAcompSim            http://expasy.nhri.org.tw/tools/aacsim/

ProfileScan             http://www.isrec.isb-sib.ch/software/PFSCAN_form.html

Prediction of secondary Structure and folding Class

nnpredict                 http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html

PredictProtein           http://www.embl-heidelberg.de/predictprotein/

SOPMA                    http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl

Prediction on Specialized Structures or Fratures

COILS                       http://www.ch.embnet.org/software/COILS_form.html

SignalP                      http://www.cbs.dtu.dk/services/SignalP/

TMAP                        http://www.mbb.ki.se/tmap/index.html

PredAcc                     http://condor.urbb.jussieu.fr/PredAccCfg.html

Structure Prediction

DALI                        http://www2.ebi.ac.uk/dali/

Swiss-Model              http://www.expasy.ch/swissmod/SWISS-MODEL.html

3D ALI                     http://www.embl-heidelberg.de/argos/ali/ali.html