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Use_OpenBabel_ver1.0

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  • 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。 http://openbabel.org/wiki/Get_Open_Babel 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。 http://www.macinchem.org/ibabel/
  • 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 (http://pubchem.ncbi.nlm.nih.gov/)・ DrugBank(http://www.drugbank.ca/)・ Online Demo - CORINA(http://www.molecular-networks.com/online_demos/corina_demo)・ DBGET Search(http://www.genome.jp/dbget-bin/www_bfind?compound)・ ZINC(http://zinc.docking.org/)4. 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 -- YASARA.org YOB format, zin -- ZINDO input format [Write-only]