Nur Shima Fadhilah Mazlan

Questions and Answers (5) View all

• Question asked in Modeling and Docking
  7 What should I look for in a visualized docked compound and what are the criteria used in finding the best docking result?
  I'm currently using AutoDock software in running my docking simulation. I had opened .dlg file to do some analysis in terms of number of hydrogen bond... [more]
  I'm currently using AutoDock software in running my docking simulation. I had opened .dlg file to do some analysis in terms of number of hydrogen bonds formed, binding energy, etc. I've also looked at reference RMSD value in .dlg file. Is it necessary to run more than 100 dockings to get a better clustering result? If we visualize the docked component, what are the important elements that we need to consider? And also for further analysis of docking result, which software do you prefer to use?
  By Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia
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• Answer added in Bioinformatics and Computational Biology
  28 Optimizing ligands before running molecular docking simulation
  By Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia
  Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia

  Thank you Dr. Mani Maran for the information given. I'm really appreciate it. 

  Thank you Dr. Mani Maran for the information given. I'm really appreciate it.
  Following
• Answer added in Bioinformatics and Computational Biology
  28 Optimizing ligands before running molecular docking simulation
  By Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia
  Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia

  Dear Dr. Mani Maran , do you think PRODRG ligand optimization is good enough than using other drawing software? I try to optimize ligand using PRODRG,... [more]

  Dear Dr. Mani Maran , do you think PRODRG ligand optimization is good enough than using other drawing software? I try to optimize ligand using PRODRG, which pdb file output is suitable for docking, currently I had chose the one with polar hydrogen. For docking, I've used AutoDock software. Btw, I really want to thanks all the comment and suggestion given. It does really help me a lot. Thank you so much..
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• Answer added in Bioinformatics and Computational Biology
  28 Optimizing ligands before running molecular docking simulation
  By Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia
  Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia

  Currently I'm using AMBER, thanks I will try to use HyperChem. Thanks.. 

  Currently I'm using AMBER, thanks I will try to use HyperChem. Thanks..
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• Question asked in Bioinformatics and Computational Biology
  28 Optimizing ligands before running molecular docking simulation
  Do I really need to optimize the ligands or redraw the ligands using software such as Marvin Sketch? If I take the ligand's structure from PUBCHEM (h... [more]
  Do I really need to optimize the ligands or redraw the ligands using software such as Marvin Sketch? If I take the ligand's structure from PUBCHEM (http://pubchem.ncbi.nlm.nih.gov/ ), do I need to optimize the ligand first? If so, which software would you recommend to do the optimization?
  By Nur Shima Fadhilah Mazlan · Universiti Teknologi Malaysia
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