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projects:software [2014/06/25 13:09]
wade [Methods and software available at other research groups]
projects:software [2019/06/07 14:32] (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. +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]].+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]]
  
-  ? [[http://​sycamore.eml.org|SYCAMORE]] 
-  : SYstems biology'​s Computational Analysis and MOdeling Research Environment 
-  ? [[http://​mcm.h-its.org/​trapp/​|TRAPP]] 
-  : a tool for analysis of transient binding pockets in proteins. 
-  ? [[http://​pipsa.h-its.org|PIPSA]] 
-  : Webserver (and software download) for comparing electrostatic potential properties of proteins structures 
-  ? [[http://​mcm.h-its.org/​sda7/​|SDA]] 
-  : Simulation of Diffusional Association - Brownian Dynamics Software 
-  ? [[http://​projects.h-its.org/​dbase/​molsurfer/​index.html|Molsurfer]] 
-  : Tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. 
-  ? [[http://​projects.h-its.org/​dbase/​ps2/​index.html|Prosat2]] 
-  : Select and group residue based annotations and explore them interactively on a 3D structure of a protein. 
-  ? [[http://​projects.h-its.org/​mcm/​software/​ramd|RAMD]] 
-  : The (RAMD) method can be used to carry out molecular dynamics simulations with an additional randomly oriented force applied to a molecule in the system. 
-    ? [[http://​projects.eml.org/​mcm/​software/​namd|NAMD]] 
-    : The Random Acceleration Molecular Dynamics (RAMD) method implemented in NAMD. 
-  ? [[http://​projects.h-its.org/​mcm/​software/​amber.html|AMBER]] 
-  : AMBER patches from the MCM group at HITS gGmbH (RAMD and NPSA) 
-  ? [[http://​projects.h-its.org/​mcm/​software/​ADS|ADS]] 
-  : Analytically Defined molecular Surfaces (used within Molsurfer). 
-  ? [[http://​projects.h-its.org/​mcmsoft/​sda/​ecm/​doc/​index.html|ECM]] 
-  : ECM is now part of the SDA distribution. 
  
 +|  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^
 +^ 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://​trapp.h-its.org|Run TRAPP analysis]] |
 +^ 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]] |
 +^ 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 ?
 +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]] |
 +^ 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]] |
 +^ 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 | ::: | ::: |
 +^ ::: | ::: | ::: | 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]] |
 +^ 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'​]] |
 +^ 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/​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]] |
  
-==== Migrated ​to other research groups ====+ 
 + 
 +==== Some software has been migrated ​to other research groups ====
   ? [[http://​ligin.weizmann.ac.il/​space/​programs/​|LIGIN]]   ? [[http://​ligin.weizmann.ac.il/​space/​programs/​|LIGIN]]
-  : Information that belongs to the article: Sobolev, V., Wade, R.C., Vriend, G. & Edelman, M. Molecular docking using surface complementarity,​ PROTEINS, 25, 120-129 (1996) ​+  : Software for molecular docking using surface complementarity,​ see: Sobolev, V., Wade, R.C., Vriend, G. & Edelman, M. Molecular docking using surface complementarity,​ PROTEINS, 25, 120-129 (1996) ​
   ? [[http://​projects.biotec.tu-dresden.de/​metapocket/​|metaPocket2]]   ? [[http://​projects.biotec.tu-dresden.de/​metapocket/​|metaPocket2]]
   : Webserver to identify pockets on protein surfaces to predict binding sites for ligands ​   : Webserver to identify pockets on protein surfaces to predict binding sites for ligands ​
  
-==== Methods and software available at other research groups ==== +==== Methods and software ​developed with participation of members of MCM are available at other research groups ==== 
-  ? [[|COMBINE analysis]]+  ? [[https://​projects.h-its.org/​mcm/​software/​|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 [[literature|Literature]] ​ [[tutorials:​tutorials|Tutorial]] [[http://​farmamol.uah.es/​index.php/​en/​2-uncategorised/​4-gcombine|gCOMBINE]]
-  ? [[|UHBD]] +  ? [[https://​projects.h-its.org/​mcm/​projects/​uppsala/​tutorials/​|UHBD]] 
-  : University of Houston Brownian Dynamics ​ [[tutorials:​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]]
   ? [[http://​www.moldiscovery.com/​soft_grid.php|GRID]]   ? [[http://​www.moldiscovery.com/​soft_grid.php|GRID]]
   : Computational method for identifying energetically favorable binding sites on biological molecules ​ [[tutorials:​tutorials|Tutorial]] ​   : Computational method for identifying energetically favorable binding sites on biological molecules ​ [[tutorials:​tutorials|Tutorial]] ​
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   ​   ​
 ==== Not updated software ==== ==== Not updated software ====
-  ? [[http://​projects.h-its.org/​dbase/​pdba/​index.html|Prosat]] +  ​? [[http://​projects.h-its.org/​mcm/​software/​amber.html|AMBER patches]] 
-  : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein. ​Currently out of date.+  : AMBER patches from the MCM group at HITS for RAMD and NPSA 
 +  ? [[http://​projects.h-its.org/​dbase/​ps2/​index.html|ProSAT2]] 
 +  : Select and group residue-based annotations and explore them interactively on a 3D structure of a protein 
 +  ​? [[http://​projects.h-its.org/​dbase/​pdba/​index.html|ProSAT]] 
 +  : Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein 
 +  ? [[https://​ligdig.h-its.org|LigDig]] 
 +  : LigDig: a web server for querying ligand–protein interactions
   ? [[http://​projects.h-its.org/​dbase/​dsmm/​|DSMM]]   ? [[http://​projects.h-its.org/​dbase/​dsmm/​|DSMM]]
   : Database of Simulated Molecular Motions   : Database of Simulated Molecular Motions
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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
 +  ​
 +===== References =====
  
  
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