Programs for analysis, imaging, and classification of proteins are far more abundant than those for nucleic acids, reflecting the diversity of structure and function of these molecules.
Included in this category are packages for searching databases (Chou-Fasman, COMBSearch, Molecules To Go), structure visualization (Chimera, HelixWheel, HyperChem, MDTOOLS, MolScript, Motif3D, Protein Explorer, PROView, Visual Molecular Dynamics, WebMol), and predicting the sites of proteolysis (CUTTER, PeptideCutter, SignalP).
Tools for predicting structural or functional domains of proteins are most abundant. These include general structure predictors/collections (ExPASy Proteomics Tools, META II, Mini-Pedant, Pfam, PRINTS, PROSPECT Pro, RAPTOR, SCOP, SOSUI, SYSTERS, TIGRFAMS, UNIPROT), fold predictors (3Matrix, FFAS03, GeneSilico), topology predictors (BPROMPT, TopPred 2, TOPS), transmembrane predictors (DAS), post-translational modification prediction (FindMod), subcellular localization prediction (LOC3d, Predotar, Psort, TargetP), phosphorylation site prediction (NetPhos, SCANSITE), mutation effects (MutaProt, Protein Mutant Database), secondary structure prediction (PsiCSI, Secondary Structure Prediction), protein side chain interactions prediction (SCWRL), and transmembrane predictions (Tbbpred, Tmpred, Transmembrane Helix Benchmark).
Other categories include motif analysis (3Motif, Gibbs Motif Sampler, Motif Analysis Workbench, Motif Scan, ParSeq), domain analysis (Biozon, ProDom, PROSITE), functional site analysis (ELM), epitope binding affinity (MHCPred), myristoylation site prediction (Myristoylator), stabilization center prediction (Stabilization Centers in Proteins), tyrosine sulfation sites (Sulfinator), and protein-protein interaction (Protein Networker).