User: sakurashirleyke

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Posts by sakurashirleyke

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During docking, should we focus on whole protein structure or only selected active sites?
... When doing docking using AutoDock Vina, there is one step : "Run Vina". This step is where we can set our "Vina Search Space".  We can set the gridbox for docking of ligands center: x, y and z size: x, y and z.   Question on, we should run the docking based on which option below? 1st Option: run ...
vina gridbox docking written 22 months ago by sakurashirleyke30 • updated 12 months ago by Biostar ♦♦ 20
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Is there any borderline of binding energy in docking stated that we should consider these ligands with its binding energy for further analysis?
... Regard virtual screening. After docking, the results will show a list of ligands with their binding energy or binding affinity. A general statement usually stated that for "binding energy / binding affinity", the more negative the energy is, the better the ligand. For example, -9.0 binding energy, w ...
virtual screening binding energy docking written 22 months ago by sakurashirleyke30 • updated 9 weeks ago by zappy0
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Reason of Removal of water molecules for protein before docking
... Commonly, during target protein preparation, it is necessary to eliminate water molecule in protein. What are the reasons to remove the non-bonded atoms which are water molecules? is it due to water molecule can affect the binding affinity? Meanwhile, is there any articles that provide the reasons o ...
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Forum: Reasons of Doing Energy Minimization and Binding Site Prediction
... What are the reasons for doing the energy minimization and binding site prediction before performing structure-based virtual screening- docking? Thank you for your kindly reply.  Hopefully can get answers from you.  :)   ...
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Steps to take before doing virtual screening
... As what i known, before doing virtual screening (Structure-based), it is commonly to do this following: 1) Energy Minimization and 2) Binding Site Prediction for the final selected model that have chosen after doing homology modelling.   However, can someone kindly tell what are the reasons for ...
forum myposts written 24 months ago by sakurashirleyke30
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Help !! Get Error when run "ANOLEA"
... Hi, when i run ANOLEA, i get this error: "Server error! The server encountered an internal error and was unable to complete your request. Error message:  Premature end of script headers: anolea.cgi " What does it mean? Does it mean my pdb file have something wrong?  Can you help me solve?. Tha ...
cgi anolea written 2.1 years ago by sakurashirleyke30 • updated 2.1 years ago by Pierre Lindenbaum99k
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Algorithm and Database or Program used by three types of different mode of SWISS-MODEL
... Hi, May I know what is the algorithm and database used by SWISS-MODEL ?.  I mean the algorithm and database used for each three type of mode which are automated mode, alignment mode and project mode.  And, according to swiss-model article, the model building of swiss-model is based on ProdMod-II or ...
online server written 2.2 years ago by sakurashirleyke30 • updated 2.2 years ago by PoGibas4.7k

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