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 and TrEMBL | タンパク質アミノ酸配列データベース |
１−２）種類別タンパク質データベース
| ENZYME (SIB) | Enzyme nomenclature database |
| PKR (SDSC) | Protein Kinase Resource |
| PROSITE (SIB) | Database of protein families and domains |
１−３）タンパク質立体構造データベース
| 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 |
| GTOP (国立遺伝研) | 全ゲノム立体構造予測データベース |
| SWISS-MODEL Repository (SIB) | A database of automatically generated protein models |
| Mod Base (Andrej Sali Lab) | a daetabase of three-dimensional protein models calculated by comparative modeling |
| LigBase (Andrej S ali Lab) | A Structural Database of Aligned Ligand Binding Sites |
１−４）その他
| Pfam (Sanger Centre) | protein domain familiy データベース |
| FSSP (EBI) | Fold classification based on Structure-Structure alignment of Proteins |
２）モチーフ／ドメイン解析
| 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 |
| MELINA (東大医科学研究所) | Motif Extraction from Promoter Regions of Potentially Co-Regulated Genes |
| YEBISU (JST) | モチーフ抽出 |
| XdomView (NUS) | A Graphical Tool for Protein Domain and Exon Position Visualization(new) |
３）２次構造予測・Assignment
| JPred(University of Dandee) | consensus 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 |
| DSSP (CmBi) | database of secondary structure assignments |
４）３次構造解析
4-1) Homology Modeling
| Swiss-Model (ExPASy) | Homology Modeling etc. |
| CPHmodels (Tech. Univ. Denmark) | predicts protein structure using comparative (homology) modelling. |
| 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(new) |
4-2) 構造比較
| CE/CL (SDSC) | Finding 3-D Similarities in Protein Structures |
| CATH (UCL) | Protein Structure Classification |
| SAWTED (Imperial Cancer Research Fund) | Structure Assignme nt With Text Description |
| 3D-PSSM (Imperial College of Science) | Protein Fold Recog nition |
| DALI (EBI) | comparing protein structures in 3D |
| SARF2 (NCI, USA) | Spatial ARangement of backbone Fragments |
| Vast Search (NCBI) | viewing superpositions and alignments by molecular graphics(new) |
| Model Quality Assessment (columbia Univ.) | Global_Assessment is a method for global quality assessment of protein models; Local_Assessment is a method for local quality assessment of protein models. |
4-3) 3D-1D/Threading
| LIBRA (国立遺伝研) | 3D-1D法 |
| 123D+ (NCI, USA) | Threading a sequence through a set of structures |
4-4) Viewer
| Protein Explorer(UMass) | Javaによる蛋白質の立体構造表示 |
| WebMol(EMBL) | Javaによる蛋白質の立体構造表示 |
５）マルチプルアライメント
| ClustalW（ゲノムネット） | 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 |
６）多目的サイト
| 新情報処理開発機構並列応用つくば研究室) | (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) |
７）その他
| 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 |
| CDART (NCBI) | Conserved Domain Architecture Retrieval Tool(new) |
| SWISS-2DPAGE (ExPASy) | Two-dimensional polyacrylamide gel electrophoresis database(new) |
| InterPre TS (EMBL) | Interaction Prediction through Tertiary Structure(new) |