Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
projects:software [2020/03/06 14:36]
richter
projects:software [2020/03/06 14:41]
richter
Line 6: Line 6:
  
 |  ^ 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]])) ​ +^ 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]] | 
- | [[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 ?
Navigation
Print/export