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projects:software [2021/02/18 07:52]
richter
projects:software [2021/02/18 15:12]
richter
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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]] |
-^ RASPD | Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, \\ Ligands | Standalone Software | (([[https://​www.frontiersin.org/​articles/​10.3389/​fmolb.2020.601065/​full|RASPD+:​ Fast protein-ligand binding free energy prediction using simplified physicochemical features.]])) | [[https://​github.com/​HITS-MCM/​RASPDplus | GitHub ]] |+^ RASPD| Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, \\ Ligands | Standalone Software | (([[https://​www.frontiersin.org/​articles/​10.3389/​fmolb.2020.601065/​full|RASPD+:​ Fast protein-ligand binding free energy prediction using simplified physicochemical features.]])) | [[https://​github.com/​HITS-MCM/​RASPDplus | GitHub ]] |
 ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://​kbbox.h-its.org|Search KBbox]] | ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver |  | [[https://​kbbox.h-its.org|Search KBbox]] |
 ^ 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 ?
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 ==== Methods and software developed with participation of members of MCM are available at other research groups ==== ==== Methods and software developed with participation of members of MCM are available at other research groups ====
-  ? [[https://projects.h-its.org/mcm/​software/|COMBINE analysis]] +  ? [[https://github.com/accsc/COMBINE|COMBINE analysis]] 
-  : Comparative Binding Energy Analysis [[literature|Literature]] ​ [[tutorials:​tutorials|Tutorial]] [[http://​farmamol.uah.es/​index.php/en/2-uncategorised/​4-gcombine|gCOMBINE]]+  : Comparative Binding Energy Analysis, extended from Ariane Nunes-Alves (MCM) and merged.  ​[[literature|Literature]] ​ [[tutorials:​tutorials|Tutorial]] [[http://​farmamol.uah.es/​soft/gCOMBINE/​|gCOMBINE ​binaries]]
   ? [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|UHBD]]   ? [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|UHBD]]
   : University of Houston Brownian Dynamics ​ [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|Tutorial]][[http://​www.chee.uh.edu/​faculty/​briggs|Contact]]   : University of Houston Brownian Dynamics ​ [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|Tutorial]][[http://​www.chee.uh.edu/​faculty/​briggs|Contact]]
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