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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:// | ^ ::: | ::: | ::: | Webserver | (([[https:// | ||
^ 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:// | ^ 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:// | ||
- | ^ RASPD | Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, \\ Ligands | Standalone Software | (([[https:// | + | ^ RASPD+ | Fast protein-ligand binding free energy prediction using simplified physicochemical features | Structures, \\ Ligands | Standalone Software | (([[https:// |
^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver | | [[https:// | ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver | | [[https:// | ||
^ 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:// | ^ 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:// | ||
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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/ | + | ? [[https://github.com/accsc/COMBINE|COMBINE analysis]] |
- | : Comparative Binding Energy Analysis [[literature|Literature]] | + | : Comparative Binding Energy Analysis, extended from Ariane Nunes-Alves (MCM) and merged. |
? [[https:// | ? [[https:// | ||
: University of Houston Brownian Dynamics | : University of Houston Brownian Dynamics |