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projects:software [2020/03/06 14:36] – richterprojects:software [2020/03/06 14:41] – richter
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 |  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ |  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^
 ^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins  | Structures, Ligands, \\ Trajectories | Webserver |  (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] | ^ TRAPP v4 | Tool for the analysis, \\ including druggability analysis, \\ of TRAnsient binding Pockets in Proteins  | Structures, Ligands, \\ Trajectories | Webserver |  (([[https://pubs.acs.org/doi/10.1021/acs.jcim.9b01185 | Druggability Assessment in TRAPP using Machine Learning Approaches]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] |
-^ TRAPP v3 | Tool for analysis of transient \\ binding pockets in proteins  | Structures, Ligands, \\ Trajectories | Standalone Software | ([[https://pubs.acs.org/doi/abs/10.1021/ci4000294 | TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins]])) | [[https://www.h-its.org/downloads/trapp/|Download TRAPP]] | +^ TRAPP v3 | Tool for analysis of transient \\ binding pockets in proteins  | Structures, Ligands, \\ Trajectories | Standalone Software | (([[https://pubs.acs.org/doi/abs/10.1021/ci4000294 | TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins]])) | [[https://www.h-its.org/downloads/trapp/|Download TRAPP]] | 
-^ ::: | ::: | ::: | Webserver |  (([[https://academic.oup.com/nar/article/45/W1/W325/3744539|TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets]]))  | [[https://trapp3.h-its.org|Run TRAPP analysis, old version]] |+^ ::: | ::: | ::: | Webserver | (([[https://academic.oup.com/nar/article/45/W1/W325/3744539 | TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets]])) | [[https://trapp3.h-its.org|Run TRAPP analysis, old version]] |
 ^ L-RIP / RIPLig | Two non-equilibrium MD approaches \\  for the  identification of \\ slow conformational changes of a \\ protein binding site​ | Protein structure | Standalone also \\ used within TRAPP |  (([[https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00101|Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets]]))  | [[http://mcm.h-its.org/lrip-riplig|L-RIP and RIPlig]] | ^ L-RIP / RIPLig | Two non-equilibrium MD approaches \\  for the  identification of \\ slow conformational changes of a \\ protein binding site​ | Protein structure | Standalone also \\ used within TRAPP |  (([[https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00101|Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets]]))  | [[http://mcm.h-its.org/lrip-riplig|L-RIP and RIPlig]] |
 ^ RAMD / \\ $\tau$RAMD| The Random Acceleration Molecular \\ Dynamics (RAMD) method can be used \\ to carry out molecular dynamics simulations \\ with an additional randomly \\ oriented force applied to a molecule \\ in the system. \\ \\ [[tauRamdDescription|see RAMD additional information]] | NAMD simulation setup | NAMD Plugin |  (([[https://www.ncbi.nlm.nih.gov/pubmed/11061976|How do substrates enter and products exit the buried active site of cytochrome P450cam ? ^ RAMD / \\ $\tau$RAMD| The Random Acceleration Molecular \\ Dynamics (RAMD) method can be used \\ to carry out molecular dynamics simulations \\ with an additional randomly \\ oriented force applied to a molecule \\ in the system. \\ \\ [[tauRamdDescription|see RAMD additional information]] | NAMD simulation setup | NAMD Plugin |  (([[https://www.ncbi.nlm.nih.gov/pubmed/11061976|How do substrates enter and products exit the buried active site of cytochrome P450cam ?

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