Your SlideShare is downloading. ×
Upcoming SlideShare
Loading in...5

Thanks for flagging this SlideShare!

Oops! An error has occurred.

Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply



Published on

Published in: Education
  • Be the first to comment

  • Be the first to like this

No Downloads
Total Views
On Slideshare
From Embeds
Number of Embeds
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

No notes for slide


  • 1. 130113 ver 1.0 OpenBabel on Mac OS X 10.6 ケモインフォマティクス関連のフリーソフトフェア。主に、 多様な化学構造フォーマットを変換するために用いられる。 Presented by Satoshi Kume, Osaka Prefecture University 1. OpenBabel のダウンロード & インストール ※ Python が必要? Macの場合、インストール済み。 2. OpenBabel のインストール確認 (ターミナル上) % which babel /usr/local/bin/babel // と表示されれば、O.K. OpenBabel のGUI版iBabelも以下のサイトで配布され ている。現在のバージョンは、iBabel 2.6。
  • 2. 3. 化学構造の取得以下のサイトで化学構造の作製・取得を行う。・ PubChem (・ DrugBank(・ Online Demo - CORINA(・ DBGET Search(・ ZINC( Babel ∼ 化学構造フォーマットの変換 ∼% babel -H // ヘルプの表示% babel [Option] [-i input-type] infile [-o output-type] outfile // 基本形% babel -i pdb AA.pdb -o mol BB.mol // PDBをMOLに変換する% babel -h AA.pdb // 水素の付加% babel -d AA.pdb // 水素の削除
  • 3. 5. 構造最適化 & エネルギー計算% obminiimze -n 2500 -ff GAFF AA.pdb > BB.pdb// GAFFによる構造 & エネルギー最適化-n 2500: default% obconformer 250 100 AA.pdb > BB.pdb// Monte Carlo searchにより250 個のランダム構造を作製した後に// 最も低いエネルギー状態を選び、100 stepsの構造最適化を行う。% obenergy -ff GAFF AA.pdb // GAFFによるエネルギー計算% obenergy -h -ff GAFF AA.pdb // 水素付加後に GAFFによるエネルギー計算使用可能な力場(-ff の後に)GAFF: General Amber Force Field (GAFF).Ghemical: Ghemical force field.MMFF94: MMFF94 force field.MMFF94s: MMFF94s force field.UFF: Universal Force Field. 複雑な化合物ほど(回転軸が多い 等)Obconformer を推奨します。6. 化合物情報の表示% obprop AA.pdb // 化学式、LogP、電荷表面積等の表示
  • 4. 7. 対応フォーマットの一覧acr -- Carine ASCI Crystal, alc -- Alchemy format, arc -- Accelrys/MSI Biosym/Insight II CAR format [Read-only], bgf --MSI BGF format, box -- Dock 3.5 Box format, bs -- Ball and Stick formatc3d1 -- Chem3D Cartesian 1 format, c3d2 --Chem3D Cartesian 2 format, caccrt -- Cacao Cartesian format, cache -- CAChe MolStruct format [Write-only], cacint --Cacao Internal format [Write-only], can -- Canonical SMILES format, car -- Accelrys/MSI Biosym/Insight II CAR format[Read-only], ccc -- CCC format [Read-only], cdx -- ChemDraw binary format [Read-only], cdxml -- ChemDraw CDXMLformat, cht -- Chemtool format [Write-only], cif -- Crystallographic Information File, cml -- Chemical Markup Language,cmlr -- CML Reaction format, com -- Gaussian 98/03 Cartesian Input [Write-only], copy -- Copies raw text [Write-only],crk2d -- Chemical Resource Kit 2D diagram format, crk3d -- Chemical Resource Kit 3D format, csr -- Accelrys/MSIQuanta CSR format [Write-only], cssr -- CSD CSSR format [Write-only], ct -- ChemDraw Connection Table format, dmol --DMol3 coordinates format, ent -- Protein Data Bank format, fa -- FASTA format [Write-only], fasta -- FASTA format [Write-only], fch -- Gaussian formatted checkpoint file format [Read-only], fchk -- Gaussian formatted checkpoint file format[Read-only], fck -- Gaussian formatted checkpoint file format [Read-only], feat -- Feature format, fh -- Fenske-Hall Z-Matrix format [Write-only], fix -- SMILES FIX format [Write-only], fpt -- Fingerprint format [Write-only], fract -- Free FormFractional format, fs -- Open Babel FastSearching database, fsa -- FASTA format [Write-only], g03 -- Gaussian 98/03Output [Read-only], g98 -- Gaussian 98/03 Output [Read-only], gam -- GAMESS Output [Read-only], gamin -- GAMESSInput [Write-only], gamout -- GAMESS Output [Read-only], gau -- Gaussian 98/03 Cartesian Input [Write-only], gjc --Gaussian 98/03 Cartesian Input [Write-only], gjf -- Gaussian 98/03 Cartesian Input [Write-only], gpr -- Ghemical format,gr96 -- GROMOS96 format [Write-only], hin -- HyperChem HIN format, inchi -- IUPAC InChI [Write-only], inp -- GAMESSInput [Write-only], ins -- ShelX format [Read-only], jin -- Jaguar input format [Write-only], jout -- Jaguar output format[Read-only], mdl -- MDL MOL format, mmd -- MacroModel format, mmod -- MacroModel format, mol -- MDL MOL format,mol2 -- Sybyl Mol2 format, molreport -- Open Babel molecule report [Write-only], moo -- MOPAC Output format [Read-only], mop -- MOPAC Cartesian format, mopcrt -- MOPAC Cartesian format, mopin -- MOPAC Internal, mopout -- MOPACOutput format [Read-only], mpc -- MOPAC Cartesian format, mpd -- Sybyl descriptor format [Write-only], mpqc -- MPQCoutput format [Read-only], mpqcin -- MPQC simplified input format [Write-only], nw -- NWChem input format [Write-only],nwo -- NWChem output format [Read-only], pc -- PubChem format [Read-only], pcm -- PCModel format, pdb -- ProteinData Bank format, pov -- POV-Ray input format [Write-only], pqs -- Parallel Quantum Solutions format, prep -- AmberPrep format [Read-only], qcin -- Q-Chem input format [Write-only], qcout -- Q-Chem output format [Read-only], report --Open Babel report format [Write-only], res -- ShelX format [Read-only], rxn -- MDL RXN format, sd -- MDL MOL format,sdf -- MDL MOL format, smi -- SMILES format, sy2 -- Sybyl Mol2 format, tdd -- Thermo format, test -- Test format [Write-only], therm -- Thermo format, tmol -- TurboMole Coordinate format, txyz -- Tinker MM2 format [Write-only], unixyz --UniChem XYZ format, vmol -- ViewMol format, xed -- XED format [Write-only], xml -- General XML format [Read-only],xyz -- XYZ cartesian coordinates format, yob -- YOB format, zin -- ZINDO input format [Write-only]