１）データベース検索 １−１）アミノ酸配列データベース
| ゲノムネット（東大・京大） | pir, Swiss-Prot, PDBSTR, PRF, etc. |
| PIR | タンパク質アミノ酸配列データベース |
| Swiss-Prot & TrEMBL | タンパク質アミノ酸配列データベース (new) |
| ENZYME (SIB) | Enzyme nomenclature database |
| HIV Protease Database (NCI) | |
| IMGT (CNRS) | international ImMunoGeneTics database |
| PKR (SDSC) | Protein Kinase Resource |
| PROSITE (SIB) | Database of protein families and domains |
| PDB（RCSB） | タンパク質立体構造データベース |
| PDB (大阪大学) | タンパク質立体構造データベース |
| SCOP (MRC) | Structural Classification of Proteins |
| SWISS-MODEL Repository (SIB) | A database of automatically generated protein models |
| Mod Base | a database of three-dimensional protein models calculated by comparative modeling |
| Pfam (Sanger Centre) | protein domain familiy データベース |
| HOMSTRAD (Univ. Cambridge) | Homologous Structur e Alignment Database |
| SPIN-PP Server (Columbia Univ.) | Surface Pro perties of INterfaces - Protein Protein Interfaces |
| FSSP (EBI) | Fold classification based on Structure-Structure alignment of Proteins (new) |
| ゲノムネット（東大・京大） | PROSITE |
| 3次元モチーフ検索（豊橋技術科学大学） | |
| Key (Columbia Univ.) | Key Residue Assignments |
| EBI | PROSITE |
| YEBISU (JST/理研GSC) | モチーフ抽出 (new) |
| JPred(EBI) | consensus method |
| PSIpred (Brunel University) | PSIPRED, MEMSAT2(transmembrane topology prediction), GenTHREADER (fold recognition method) |
| Prof (University of Wales) | Secondary Structure Prediction using Cascaded Mutiple Classifers |
| NNPREDICT (UCSF) | ニューラルネットワーク |
| PHD (EMBL) | ニューラルネットワーク＆マルチプルアラインメント |
| PREDATOR (EMBL) | ニューラルネッ トワーク＆マルチプルアラインメント |
| SOSUI（東京農工大・生命工学科） | 膜タンパクの２次構造予測 |
| TMHMM (CBS, The Technical University of Denmark) | Prediction of transmembrane helices in proteins |
| SSThread（国立遺伝研） | 3D-1D法による蛋白質の２次構造予測 |
| CE/CL (SDSC) | Finding 3-D Similarities in Protein Structures |
| CATH (UCL) | Protein Structure Classification |
| SAWTED (Imperial Cancer Research Fund) | Structure Assignment With Text Description |
| 3D-PSSM (Imperial Cancer Reseach Fund) | Protein Fold Recognition |
| CPHmodels (Tech. Univ. Denmark) | predicts protein structure using comparative (homology) modelling. |
| DALI (EBI) | comparing protein structures in 3D |
| Fold Recognition Server (UCLA) | Protein Fold Recognition |
| LIBRA (国立遺伝研) | 3D-1D法 |
| Swiss-Model (ExPASy) | Homology Modeling etc. |
| PHD Threader (EMBL-heidelberg) | Prediction-based threading |
| SAM-T98 (UCSC) | Sequence Alignment and Modeling System using HMM |
| ゲノムネット（東大・京大） | clustalW |
| 国立遺伝研 | 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 (東大・医科学研究所/埼玉県立ガンセンター) | 高感度マルチプルアラインメントプログラム (new) |
| 新情報処理開発機構並列応用つくば研究室) | 並列タンパク質情報解析システム (構造検索・相同性検索・マルチプルアライメント 二次構造予測・転写因子結合部位予測 PDB代表タンパク質チェインDB) |
| 3DALIGN (HGC) | protein structure alignment |
| Family Pairwise Search (SDSC, UCSC) | protein family classification |
| GeneFIND (PIR/Univ. of Texas Health Center at Tyler) | Protein Family の Identification |
| PredAcc (INSERM U155) | 側鎖の solvent accessibility 予測 |
| GRASS Browser (Columbia Univ.) | Graphical Representation and Analysis of Structure Server |
| SignalP (CBS, The Technical University of Denmark) | signal peptide cleavage sites 予測 |
| PSORT（東大・医科学研究所） | Protein Sorting Signal と Localization Site の予測 |