Links: Analysis（解析ツール）
Sequence（配列情報）
| Link | Outline |
|---|---|
| BLAST | Tool for finding regions of similarity between biological sequences. The query is either nucleotide or protein sequence. A sequence hit with E-values of 0.001 may be significant. |
| ClustalW | Tool for multiple sequence alignment. The query is a sequence. |
| ESPript | A easy-to-use program that renders sequence similarities and secondary structural information from aligned protein sequences |
| ENDscript | A Web server that extracts and renders a comprehensive analysis of primary to quaternary protein structure information. The query is the PDB ID of a target protein. A set of protein structures (tagged with PDB ID) can be extracted using ENDscript, and its output can be further modified with the ADV mode of ESPript. |
| Translate | This tool allows us to translate a nucleotide (DNA/RNA) sequence to a protein sequence. When you want both sequence at one time, select the option "Includes nucleotide sequence" in "Output format" tab. |
| Codon Usage Database | The codon usage table of an organism can be obtained in this web site. Also, a codon usage can be calculated using a nucleotide sequence. |
| ProtScale | ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein. |
| GRAVY (Grand average hydropathy) index | GRAVY index is one of the few key sequence-derived attributes affecting the successful outcome of crystallization effort. |
Structure（立体構造）
| Link | Outline |
|---|---|
| Dali server | Comparing protein structures in 3D. This may reveal biologically interesting similarities that are not detectable by comparing sequences. |
| Dali pairwise comparison | Superimposing two particular structures |
| PsiPred | Protein secondary structure prediction |
| Consurf | Finding evolutionary conservation profiles for proteins of known structure in the PDB |
| Evolutionary Trace | Evolutionary Trace (ET) assigns to each sequence residue a relative score of "functional importance". This score infers the molecular determinants of activity and specificity. |
| UCSF CHIMERA | A program for the interactive visualization and analysis of molecular structures and related data, including density maps, sequence alignments, docking results, and trajectories. |
| 統合TV：タンパク質配列・構造解析 | タンパク質の解析法について動画で知ることができます。 |
| 創薬等支援基盤プラットフォーム | 構造生物学のツールとデータベースを検索できる |
| Sasaki Table | X-ray Absorption and Emission Table |
| HIC-Up | Database for a low-molecular weight compound |
| DichoWeb | On-line analysis of protein CD spectrum |
| Windowsで行こう 構造生物学に関する備忘録 | Pymol, CCP4-mgなど構造生物学的解析でよく使うソフトの使い方が詳しく書かれています。知りたいことが書かれていて、大変参考になります。 |
| 東京大学・農学部・酵素学研究室・リンク集 | 伏信進矢先生がまとめられたリンク集。迷ったらこのリンク集で手がかりを探します。非常に有り難い情報源です。 |
| 東京大学・農学部・酵素学研究室・マニュアル集 | 伏信進矢先生がまとめられたマニュアル集。プログラムを使用した記録を書いてくださっているので、とても有り難いです。 |
