Activity for Sherif Elsabbagh
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Sherif Elsabbagh posted a comment on discussion Help and Feedback
thanks so much.. because I always use open babel to generate 3D conformer with --minimize .. but someone mentioned that you do not need this. just convert to 3D..
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I know this might be a very basic question. But I need to make sure. Before using smina, is it really necessary to minimize ligands ? Because I read somewhere else a comment saying that ligand energy minimization is not that necessary
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perfect i will try it thanks so much
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perfect i will try it thanks so much
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sorry i didnt know that.. so you mean to apply other docking softwares and use consensus docking scores.. but nothing can be changed within smina itself..
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Hi I have a question. I tried to validate the docking experiment by first running docking of actives and decoys against the target protein. I drawed the ROC and the AUC was calculated as 0,65.. In this case, what can be done to improve this score. How can i manipulate the software to enhance the score thanks
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Hi again.. I managed to find another tool called sdsort but when i use it I have a txt file like this REC minimizedAffinity 001 -10.807 0.000 002 -10.192 0.000 003 -10.044 0.000 004 -10.043 0.000 005 -9.874 0.000 006 -9.844 0.000 007 -9.796 0.000 008 -9.742 0.000 009 -9.698 0.000 010 -9.671 0.000 011 -9.567 0.000 012 -9.490 0.000 013 -9.449 0.000 014 -9.430 0.000 015 -9.407 0.000 016 -9.392 0.000 017 -9.280 0.000 018 -9.102 0.000 019 -9.098 0.000 020 C -9.088 0.000 021 C077 -9.066 0.000 022 -9.064...
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sorry for all these questions but I cant find any other alternative to this tool
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i have Big sur 11.5.2 i install these libraries using homebrew and conda
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g++ main.cpp CommandLine2/CommandLine.cpp -L/usr/local/lib -O3 -g -o Release/sdsorter -I/usr/local/include/openbabel3 -I/usr/include/openbabel3 -lopenbabel -lboost_system -lboost_regex -lboost_filesystem -lboost_iostreams ld: warning: dylib (/usr/local/lib/libopenbabel.dylib) was built for newer macOS version (11.0) than being linked (10.16) ld: warning: dylib (/usr/local/lib/libboost_system.dylib) was built for newer macOS version (11.0) than being linked (10.16) ld: warning: dylib (/usr/local/lib/libboost_regex.dylib)...
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i am very sorry.. but i didnt understande where to fix this? is there anything that can do same function as sdsorter?
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thanks for your comment.. can you tell me how to build it from source.. i just downloaded sdsorter.osx and run it using ./sdsorter.osx after giving permission to it. is there any other tool that can give the same result ?
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when i tried to use sdosrter i got this message dyld: Library not loaded: /opt/local/lib/libopenbabel.5.dylib Referenced from: /Users/sherifelsabbagh/opt/anaconda3/envs/my-rdkit-env/bin/sdsorter.osx Reason: image not found although i installed the latest version of obabel.. can you help me with this?
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