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projects:software [2019/06/07 09:36]
richter
projects:software [2019/09/18 13:04] (current)
richter
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 {{:​projects:​mcm_logo.jpg}} {{:​projects:​mcm_logo.jpg}}
-====== MCM software and databases ​======+===== MCM software and databases =====
 This page has links for webservers and software downloads provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS). This page has links for webservers and software downloads provided by the Molecular and Cellular Modeling (MCM) group at the Heidelberg Institute for Theoretical Studies (HITS).
 There are tutorials for some software on our [[tutorials:​tutorials|tutorials page]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]] There are tutorials for some software on our [[tutorials:​tutorials|tutorials page]]. For queries, send email to: [[mcmsoft@h-its.org|mcmsoft@h-its.org]]
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 ^ TRAPP v4 | Tool for druggability analysis of transient \\ binding pockets in proteins ​ | Structures, Ligands, \\ Trajectories | Webserver | | not yet released | ^ 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. \\ \\ For additional information  +^ 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 ? 
- \\ [[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 \\ (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 |  (([[Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations.|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]] | +^ 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]] |+
 ^ ::: | ::: | ::: | Webserver |  (([[http://​dx.doi.org/​10.1093/​nar/​gkv335|webSDA:​ a web server to simulate macromolecular diffusional association.]])) ​ | [[https://​websda.h-its.org|Run webSDA]] | ^ ::: | ::: | ::: | Webserver |  (([[http://​dx.doi.org/​10.1093/​nar/​gkv335|webSDA:​ a web server to simulate macromolecular diffusional association.]])) ​ | [[https://​websda.h-its.org|Run webSDA]] |
-^ PIPSA / \\ webPIPSA | Comparing electrostatic potentials \\ (or other molecular interaction fields)\\ of protein structures | Protein Structures \\ of the same fold | Standalone Software |  (([[http://www3.interscience.wiley.com/cgi-bin/abstract/80002581/ABSTRACT|Protein Interaction Property Similarity Analysis. ]])) (([[http://​www.biomedcentral.com/​1471-2105/​8/​373/​|qPIPSA:​ Relating enzymatic kinetic parameters and interaction fields]])) ​ | [[https://​projects.h-its.org/​mcmsoft/​pipsa/​4.0.2/​availability.html|Download PIPSA/​Multipipsa]] |+^ PIPSA / \\ webPIPSA | Comparing electrostatic potentials \\ (or other molecular interaction fields)\\ of protein structures | Protein Structures \\ of the same fold | Standalone Software |  (([[https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.1204|Protein Interaction Property Similarity Analysis. ]])) (([[http://​www.biomedcentral.com/​1471-2105/​8/​373/​|qPIPSA:​ Relating enzymatic kinetic parameters and interaction fields]])) ​ | [[https://​projects.h-its.org/​mcmsoft/​pipsa/​4.0.2/​availability.html|Download PIPSA/​Multipipsa]] |
 ^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: | ^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: |
-^ ::: | ::: | ::: | Webserver |  (([[http://nar.oxfordjournals.org/cgi/content/abstract/gkn181|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.eml.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.]])) ​ | [[http://​prosat.h-its.org/​prosat/​prosatexe?​pdbcode=1o1o|Hemoglobin example '​1o1o'​]] | +^ 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]])) ​ (([[http://nar.oupjournals.org/cgi/content/full/31/13/3349|MolSurfer: a macromolecular interface navigator.]])) ​ | [[https://​molsurfer.h-its.org/​demo/​1nca/​result.html|Neuraminidase 1nca example]] |+^ 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]] | ^ 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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   : Scripts for pKa calculations with UHBD   : Scripts for pKa calculations with UHBD
   ​   ​
-==== References ====+===== References ​=====
  
  
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