Protein Secondary Tertiary Structure Prediction (SSP)
 
123D
2ZIP - Server leucine zipper prediction
3D-JIGSAW - Protein Comparative Modeling Server
3D-pssm
A Guide to Structure Prediction
Abagyan Group
ANTHEPROT
Baker Lab
BCM Search Launcher
BioCoRE - A Biological Collaborative Research Environment
CDART - Conserved Domain Architecture Retrieval Tool
Chime
Chou Fasman (@BMERC)
City of Hope
Cn3D - NCBI's 3D structure viewer
columba
Compare & Align 3D Protein Structures
Computational Genomics Group
Dali (EBI)
Dimitrios Morikis (UCR)
ESyPred3D - Predict Protein 3D Structure
ExPASy Proteomics Tools
FFAS (Burnham Institute)
FSSP documentation
FSSP table
FUGUE - Align Sequences Against Structures
GENO3D - Modeling of 3D Protein Stucture
HMMTOP - Transmembrane & Topology Prediction
HOMSTRAD - Homologous Structure Alignment Database
Honig Lab
Insight II (Accelrys) 
Jackal: protein structure modeling package
JPRED (Barton Group)
List of Tools
MOTIF - Protein & Nucleic Acide Sequence Motif Search
MRC Mathmatical Biology
NCBI Structure Group
NCBI VAST - Vector Alignment Search Tool
NNPREDICT - Protein Secondary Structure Prediction
nnPredict (UCSF)
PeptIdent - Identify Proteins
Pov-Chem (visualization of chemicals)
Pov-Chem (visualization of chemicals)
Pov-Ray
PREDATOR
Prediction Protein-3D Structures
Prediction Servers for DNA & Protein Sequences
PredictProtein
PROSPECT
Protein Fold Prediction
Protein Structural Analysis (@BMERC)
Protein Topology home page (@ EBI)
ProtFun Server
PSIPRED Protein Structure Prediction Server
PSORT
Rasmol (download)
SBASE Structure Prediction
SCOP: Structural Classification of Proteins
SeqAnalRef (ExPASy)
Sequence Analysis wwwTools
SignalP - Predicts Signal Peptides
SMART - Simple Molecular Architecture Research Tool
Software to Analyze NPS@ Data
SSP at BMERC (Boston) -
Structure Prediction Meta Server (Polish Bioinformatics Site)
SubLoc - Prediction of Protein Subcellular Localization
SWISS-MODEL - Protein Modeling Server
The PredictProtein Server
The PSIPRED Protein Structure Prediction Server
The Tree of Life Home Page
TMHMM Server - Transmembrane Prediction
TOPITS (EMBL)
TOPS (Topology Atlas @ EBI)
Tripos, Inc.
Tripos, Inc.
UCLA/DOE Fold Server
UCLA-DOE Structure Prediction Server
VAST - Retrieve structure alignments froom NCBI