A Practical Guide to Cancer Systems Biology
Protein Structure Modeling 119 VIII. Read the text below ‘Search for Templates’. If you accept the term below, hit ‘Search for ...
120 A Practical Guide to Cancer Systems Biology Figure 4. Modeling with I-tasser Web. (a) Job submission form of I-tasser. (b) R ...
Protein Structure Modeling 121 Figure 5. Modeling with ModWeb. (a) ModWeb job submitting form. (b) Result page, notifying you ...
122 A Practical Guide to Cancer Systems Biology It’s highly recommended that you fill in your e-mail address into the form, sinc ...
Protein Structure Modeling 123 Figure 6. Quality assessment with QMean server. (a) Job submission page and (b) evaluation repo ...
124 A Practical Guide to Cancer Systems Biology Figure 7. Sequence identity information (marked by black box) can be obtained fr ...
Protein Structure Modeling 125 Figure 8. Evaluate model with ModEval. (a) Job submission form and (b) result page, containing ...
126 A Practical Guide to Cancer Systems Biology Figure 9. Screenshot of PyMol application. Black box and white box indicates the ...
Protein Structure Modeling 127 V. Use‘png’command to save your figures: png molecularimage.png width=640 height=480 ray=1 If y ...
11. Docking Simulation Chia-Hsien Lee and Hsueh-Fen Juan∗ Graduate Institute of Biomedical Electronics and Bioinformatics, Natio ...
130 A Practical Guide to Cancer Systems Biology In essence, it accepts a protein structure file, a compound structure file, and ...
Docking Simulation 131 Get ligand structures from PubChem Here we’ll guide you to query PubChem6,7and download your query resu ...
132 A Practical Guide to Cancer Systems Biology Procedure I. Navigate to PubChem by using its URL (https://pubchem.ncbi. nlm.nih ...
Docking Simulation 133 (a)(b) (c) Figure 3. Searching ligands from ZINC database. (a) ZINC entrance interface. (b) ZINC search ...
134 A Practical Guide to Cancer Systems Biology the bar under the large “ZINC” logo. A small panel will pop up and showing all p ...
Docking Simulation 135 (a)(b) (c) Figure 4. Subset listing of ZINC database (a) by catalog, (b) by property and (c) subset inf ...
136 A Practical Guide to Cancer Systems Biology (a)(b) Figure 5. Download DrugBank database. (a) Entrance page. (b) Database dow ...
Docking Simulation 137 For Microsoft Windows users, installing MSYS system (from http:// http://www.mingw.org/wiki/msys),,) Cy ...
138 A Practical Guide to Cancer Systems Biology III. Load the protein structure file into a molecular editor (e.g., PyMol) and r ...
Docking Simulation 139 centerz=−2.5 sizex=10 sizey=10 sizez=10 energyrange = 4 exhaustiveness = 16 Modify the fields when need ...
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