1) Detabase Search
1-1) Amino Acid Sequence Databases
| Genome Net (The University of Tokyo and Kyoto university) | Pir, Swiss-Prot, PDBSTR, PRF, etc. |
| PIR | Protein sequence database |
| Swiss-Prot and TrEMBL | Protein sequence database |
1-2) Protein Database on Each Protein family
| ENZYME (SIB) | Enzyme nomenclature database |
| PKR (SDSC) | Protein kinase resource |
| PROSITE (SIB) | Database of protein families and domains |
1-3) Protein 3D Structure Database
| PDB(RCSB) | Database of protein 3D structures |
| PDBj (Osaka University) | Database of protein 3D structures |
| SCOP (MRC) | Structural classification of proteins |
| GTOP (National Institute of Genetics) | Genomes to protein structures and functions |
| SWISS-MODEL Repository (SIB) | Database of automatically generated protein models |
| Mod Base (Andrej Sali Lab) | Database of 3D protein models calculated by comparative modeling |
1-4) Others
| Pfam (Sanger Centre) | Protein domain familiy database |
| HOMSTRAD (Univ. Cambridge) | Homologous structure alignment database |
| SPIN-PP Server (Columbia Univ.) | Surface properties of interfaces: Protein-protein Interfaces |
| FSSP (EBI) | Fold classification based on structure-structure alignment of proteins |
2) Motif and Domain Analysis
| Genome Net (The University of Tokyo and Kyoto University) | PROSITE |
| 3D motif search (Toyohashi University of Technology) | |
| Key (Columbia Univ.) | Key residue assignments |
| EBI | PROSITE |
| MELINA (The Institute of Medical Science, The University of Tokyo) | Motif extraction from promoter regions of potentially co-regulated genes |
| YEBISU (JST) | Motif extracion |
| XdomView (NUS) | Graphical tool for protein domain and exon position visualization |
3) 2D Structure Prediction and Assignment
| JPred(University of Dandee) | Cconsensus method |
| Prof (University of Wales) | 2D structure prediction using cascaded mutiple classifers |
| NNPREDICT (UCSF) | Neural network |
| PHD (EMBL) | Neural network & multiple alignment |
| PREDATOR (EMBL) | Neural Network & Multiple Alignment |
| SOSUI（Tokyo University of Agriculture and Technology） | 2D structure prediction for membrane protein |
| TMHMM (CBS, The Technical University of Denmark) | Prediction of transmembrane helices in proteins |
| SSThread (National Institute of Genetics) | 2D structure prediction by using 3D-1D method |
| DSSP (CmBi) | Database of 2D structure assignments |
4) 3D Structural Analysis
4-1) Homology Modeling
| Swiss-Model (ExPASy) | Homology modeling etc. |
| CPHmodels (Tech. Univ. Denmark) | Predicts protein structure using comparative (homology) modeling |
| SAM-T98 (UCSC) | Sequence alignment and modeling system using HMM |
| joy (University of Cambridge) | Protein structure and alignment analysis |
| ESyPred3D | (The University of Namur) |
| SDSC1 (San Diego Supercomputer Center) | Homology modeling |
| 3D-JIGSAW (ICRF) | Homology modeling |
| Geno3D (PBIL) | Homology modeling |
4-2) Structural Comparison
| CE/CL (SDSC) | Finding 3D similarities in protein structures |
| CATH (UCL) | Protein structure classification |
| SAWTED (Imperial Cancer Research Fund) | Structure assignment with text description |
| 3D-PSSM (Imperial College of Science) | Protein fold recognition |
| DALI (EBI) | Comparing 3D protein structures |
| SARF2 (NCI, USA) | Spatial arrangement of backbone fragments |
| Vast Search (NCBI) | Viewing superpositions and alignments by molecular graphics |
4-3) 3D-1D/Threading
| LIBRA (National Institute of Genetics) | 3D-1D method |
| 123D+ (NCI, USA) | Threading a sequence through a set of structures |
4-4) Viewers
| Protein Explorer(UMass) | Display of Protein 3D structure by using Java |
| WebMol(EMBL) | Display of Protein 3D structure by using Java |
5) Multiple Alignment
| ClustalW（Genome Net） | clustalW |
| National Institute of Genetics | clustalW |
| AMAS (EBI) | Analyse multiply aligned sequences |
| Jalview (EBI) | java multiple alignment editor |
| CINEMA (University of Manchester) | Colour interactive editor for multiple alignments |
| The University of Namur (Belgium) | Match_Box |
| Parallel PRRN (The Institute of Medical Science, The University of Tokyo/Saitama Cancer Center) | High sensitivity multiple alignment program |
6) Multipurpose Sites
| PAPIA (AIST) | Structure search, Homology search, Multiple alignment, 2D Structure prediction, and so on. |
7) Others
| 3DALIGN (HGC) | Protein structure alignment |
| Family Pairwise Search (SDSC, UCSC) | Protein family classification |
| GeneFIND (PIR/Univ. of Texas Health Center at Tyler) | Identification of protein family |
| PredAcc (INSERM U155) | Prediction of sidechain solvent accessibility |
| GRASS Browser (Columbia Univ.) | Graphical representation and analysis of structure server |
| SignalP (CBS, The Technical University of Denmark) | Prediction of signal peptide cleavage sites |
| PSORT（The Institute of Medical Science, The University of Tokyo） | Prediction of protein sorting signal and localization sites |
| CDART (NCBI) | Conserved domain architecture retrieval tool |
| SWISS-2DPAGE (ExPASy) | Two-dimensional polyacrylamide gel electrophoresis database |
| InterPre TS (EMBL) | Interaction prediction through 3D structures |