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projects:software [2019/09/18 13:04] richter |
projects:software [2020/03/06 14:18] 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 druggability analysis of transient \\ binding pockets in proteins | Structures, Ligands, \\ Trajectories | Webserver | | | | ||
| ^ 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://trapp.h-its.org|Run TRAPP analysis]] | | ^ ::: | ::: | ::: | Webserver | (([[https://academic.oup.com/nar/article/45/W1/W325/3744539|TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets]])) | [[https://trapp.h-its.org|Run TRAPP analysis]] | | ||
| - | ^ TRAPP v4 | Tool for druggability analysis of transient \\ binding pockets in proteins | Structures, Ligands, \\ Trajectories | Webserver | | not yet released | | ||
| ^ 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 ? | ||
