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| ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ | | ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^ | ||
+ | ^ Molsurfer | Protein structure tool \\ to link a 2D projection of a \\ macromolecular interface to a 3D \\ view of the macromolecular structures \\ [[http://projects.h-its.org/mcm/software/ADS|ADS]] Analytically Defined molecular Surfaces \\ is used within Molsurfer | PDB/PQR files \\ or PDB codes | Webserver | (([[https://projects.h-its.org/dbase/molsurfer/doc/tibs.html|MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes]])) (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/|MolSurfer: a macromolecular interface navigator.]])) | [[https://molsurfer.h-its.org]] \\ [[https://molsurfer.h-its.org/demo/1nca/result.html|Neuraminidase 1nca example]] | | ||
^ 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]])) | [[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://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 ? | + | ^ 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]] | | ||
+ | ^ 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]] | | ||
- | ^ ::: | ::: | ::: | GROMACS RAMD\\ implementation | ((to be filled)) | [[https://github.com/HITS-MCM/gromacs-ramd]] \\ [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/|RAMD in GROMACS Tutorial]] | | + | ^ ::: | ::: | ::: | GROMACS RAMD\\ implementation | (([[https://arxiv.org/abs/2006.11066|Kokh DB et. al. A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories. arXiv 2020 arXiv:2006.11066]])) | [[https://github.com/HITS-MCM/gromacs-ramd]] \\ [[https://kbbox.h-its.org/toolbox/tutorials/estimation-of-relative-residence-times-of-protein-ligand-complexes-using-random-acceleration-molecular-dynamics-ramd-implementation-in-gromacs/|RAMD in GROMACS Tutorial]] | |
^ MD-IFP | MD trajectory analysis using protein-ligand Interaction Fingerprints | Trajectories \\ Test dataset provided | Jupyter Notebooks | (([[https://arxiv.org/abs/2006.11066|IFP analysis of dissociation trajectories for 3 compounds of HSP90 reported in the paper D. B. Kokh, B. Doser, S. Richter, F. Ormersbach, X. Cheng , R.C. Wade "A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories" (2020) submitted to JCP]])) | [[https://github.com/HITS-MCM/MD-IFP]]| | ^ MD-IFP | MD trajectory analysis using protein-ligand Interaction Fingerprints | Trajectories \\ Test dataset provided | Jupyter Notebooks | (([[https://arxiv.org/abs/2006.11066|IFP analysis of dissociation trajectories for 3 compounds of HSP90 reported in the paper D. B. Kokh, B. Doser, S. Richter, F. Ormersbach, X. Cheng , R.C. Wade "A Workflow for Exploring Ligand Dissociation from a Macromolecule: Efficient Random Acceleration Molecular Dynamics Simulation and Interaction Fingerprints Analysis of Ligand Trajectories" (2020) submitted to JCP]])) | [[https://github.com/HITS-MCM/MD-IFP]]| | ||
^ SDA / \\ webSDA | Simulation of Diffusional Association - \\ Brownian Dynamics Software \\ [[https://mcm.h-its.org/sda/doc/doc_sda7/ecm.html|ECM]] is part of the SDA distribution \\ and allows the \\ calculation of partial charges. | Structures of \\ Solutes | Standalone Software | (([[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23971|SDA 7: A modular and parallel implementation of the simulation of diffusional association software]])) | [[https://www.h-its.org/downloads/sda7/|Download SDA]] | | ^ SDA / \\ webSDA | Simulation of Diffusional Association - \\ Brownian Dynamics Software \\ [[https://mcm.h-its.org/sda/doc/doc_sda7/ecm.html|ECM]] is part of the SDA distribution \\ and allows the \\ calculation of partial charges. | Structures of \\ Solutes | Standalone Software | (([[https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23971|SDA 7: A modular and parallel implementation of the simulation of diffusional association software]])) | [[https://www.h-its.org/downloads/sda7/|Download SDA]] | | ||
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^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | | ^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | | ||
^ ::: | ::: | ::: | Webserver | (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447742/|webpipsa: a web server for the comparison of protein interaction properties.]])) | [[https://pipsa.h-its.org|Run Pipsa Analysis]] | | ^ ::: | ::: | ::: | Webserver | (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447742/|webpipsa: a web server for the comparison of protein interaction properties.]])) | [[https://pipsa.h-its.org|Run Pipsa Analysis]] | | ||
- | ^ Sycamore | SYstems biology's Computational \\ Analysis and MOdeling Research Environment | Kinetic Data | Webserver | (([[https://academic.oup.com/bioinformatics/article/24/12/1463/196145|SYCAMORE-a systems biology computational analysis and modeling research environment.]])) | [[http://sycamore.eml.org|Sycamore webserver]] | | + | ^ Sycamore | SYstems biology's Computational \\ Analysis and MOdeling Research Environment | Kinetic Data | Webserver | (([[https://academic.oup.com/bioinformatics/article/24/12/1463/196145|SYCAMORE-a systems biology computational analysis and modeling research environment.]])) | [[http://sycamore.h-its.org|Sycamore webserver]] | |
- | ^ ProSAT+ | Protein structure visualization and \\ annotation tool. \\ Display protein annotations \\ (eg mutation data from uniprot) \\ on protein structures from RCSB. | PDB or Uniprot codes | Webserver | (([[http://dx.doi.org/10.1093/protein/gzw021|ProSAT+: visualizing sequence annotations on 3D structure.]])) | [[https://prosat.h-its.org|https://prosat.h-its.org]] \\ [[https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o1o|Hemoglobin example '1o1o']] | | + | |
- | ^ Molsurfer | Protein structure tool \\ to link a 2D projection of a \\ macromolecular interface to a 3D \\ view of the macromolecular structures \\ [[http://projects.h-its.org/mcm/software/ADS|ADS]] Analytically Defined molecular Surfaces \\ is used within Molsurfer | PDB/PQR files \\ or PDB codes | Webserver | (([[https://projects.h-its.org/dbase/molsurfer/doc/tibs.html|MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes]])) (([[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168994/|MolSurfer: a macromolecular interface navigator.]])) | [[https://molsurfer.h-its.org]] \\ [[https://molsurfer.h-its.org/demo/1nca/result.html|Neuraminidase 1nca example]] | | + | |
- | ^ KBbox | KBbox: a Toolbox of \\ Computational Methods for Studying \\ the Kinetics of Molecular Binding | Search term | Webserver | | [[https://kbbox.h-its.org|Search KBbox]] | | + | |
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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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? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] | ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]] | ||
: Scripts for pKa calculations with UHBD | : Scripts for pKa calculations with UHBD | ||
+ | ? ProSAT+ Protein structure visualization and \\ annotation tool. | ||
+ | :[[https://prosat.h-its.org|ProSAT+ retired]] | ||
+ | |||
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===== References ===== | ===== References ===== | ||