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projects:software [2020/07/23 08:21]
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projects:software [2020/07/23 08:22] (current)
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 ^ ::: | ::: | ::: | 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. Originally this was implemented \\ from the MCM group in Amber 8 (not maintained). Recently the Amber group has provided the \\ functionality integrated in Amber 20 \\ [[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. Originally this was implemented \\ from the MCM group in Amber 8 (not maintained). Recently the \\ Amber group has provided the functionality integrated in Amber 20 \\ [[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 ?
 1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms]])) (([[https://​link.springer.com/​article/​10.1007/​s008940050053|Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data]])) ​ | Included in NAMD \\ distribution (plugin directory) \\ also here with \\ additional resources \\ [[https://​www.h-its.org/​downloads/​ramd|Download]] |  1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms]])) (([[https://​link.springer.com/​article/​10.1007/​s008940050053|Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data]])) ​ | Included in NAMD \\ distribution (plugin directory) \\ also here with \\ additional resources \\ [[https://​www.h-its.org/​downloads/​ramd|Download]] | 
 ^ ::: | ::: | ::: | $\tau$RAMD scripts |  (([[https://​pubs.acs.org/​doi/​10.1021/​acs.jctc.8b00230|Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.]])) (([[https://​www.frontiersin.org/​articles/​10.3389/​fmolb.2019.00036/​full|Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times.]])) ​ | Includes ​ RAMD plugin \\ with additional scripts \\ [[https://​www.h-its.org/​downloads/​ramd|Download]] | ^ ::: | ::: | ::: | $\tau$RAMD scripts |  (([[https://​pubs.acs.org/​doi/​10.1021/​acs.jctc.8b00230|Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.]])) (([[https://​www.frontiersin.org/​articles/​10.3389/​fmolb.2019.00036/​full|Machine learning analysis of tauRAMD trajectories to decipher molecular determinants of drug-target residence times.]])) ​ | Includes ​ RAMD plugin \\ with additional scripts \\ [[https://​www.h-its.org/​downloads/​ramd|Download]] |
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