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--- projects:software [2018/02/12 11:05]
richter [Current software of the Group]
+++ projects:software [2019/09/18 13:04] (current)
richter
@@ Line 1: / Line 1: @@
 {{: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).
 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]]
-==== Current software of the Group ====
-  ? [[http://kbbox.h-its.org/toolbox|KBbox]]
-  : KBbox: a Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding
-  ? [[http://mcm.h-its.org/ligdig|LIGDIG]]
-  : LigDig: a web server for querying ligand–protein interactions
-  ? [[http://sycamore.eml.org|SYCAMORE]]
-  : SYstems biology's Computational Analysis and MOdeling Research Environment
-  ? [[http://mcm.h-its.org/trapp/|TRAPP]]
-  : Tool for analysis of transient binding pockets in proteins
-  ? [[http://pipsa.h-its.org|PIPSA]]
-  : Webserver (and software download) for comparing electrostatic potentials (or other molecular interaction fields) of protein structures
-  ? [[http://mcm.h-its.org/sda7/|SDA]]
-  : Simulation of Diffusional Association - Brownian Dynamics Software
-  ? [[http://mcm.h-its.org/websda|webSDA]]
-  :Webserver for Simulation of Diffusional Association
-  ? [[http://mcm.h-its.org/lrip-riplig|L-RIP and RIPlig]]
+|  ^ Description ^ Input ^ Type ^ Main \\ Refer- \\ ence(s) ^ Link ^
-  : Two non-equilibrium MD approaches  for the  identification of slow conformational changes of a protein binding site
+^ 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]] |
-  ? [[http://projects.h-its.org/dbase/molsurfer/index.html|Molsurfer]]
+^ ::: | ::: | ::: | 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]] |
-  : Tool to link a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures
+^ TRAPP v4 | Tool for druggability analysis of transient \\ binding pockets in proteins  | Structures, Ligands, \\ Trajectories | Webserver | | not yet released |
-  ? [[http://prosat.h-its.org/|ProSAT]]<sup>+</sup>
+^ 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]] |
-  : Display protein annotations on protein structures. Click to start hemoglobin example '1o1o' in [[http://prosat.h-its.org/prosat/prosatexe?pdbcode=1o1o|Protein structure visualization and annotation tool]]. ProSAT<sup>+</sup> is also listed on [[https://omictools.com/protein-structure-annotation-tool-plus-tool|OMICs Tools collection]]
+^ 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 ?
-  ? [[http://projects.h-its.org/mcm/software/ramd|RAMD]]
+. 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]] |
-  : 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
+^ ::: | ::: | ::: | $\tau$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]] |
-  ? [[http://projects.eml.org/mcm/software/namd|RAMD in NAMD]]
+^ 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]] |
-  : The RAMD method implemented in NAMD
+^ ::: | ::: | ::: | 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]] |
-  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]]
+^ 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]] |
-  : AMBER patches from the MCM group at HITS for RAMD and NPSA
+^ ::: | ::: | ::: | Python Interface \\ Multipipsa | ::: | ::: |
-  ? [[http://projects.h-its.org/mcm/software/ADS|ADS]]
+^ ::: | ::: | ::: | 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]] |
-  : Analytically Defined molecular Surfaces (used within Molsurfer)
+^ 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]] |
-  ? [[http://mcm.h-its.org/sda/doc/doc_sda7/ecm.html|ECM]]
+^ 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']] |
-  : ECM is now part of the SDA distribution
+^ 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]] |
-==== Migrated to other research groups ====
+==== Some software has been migrated to other research groups ====
   ? [[http://ligin.weizmann.ac.il/space/programs/|LIGIN]]
   : 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)
@@ Line 44: / Line 31: @@
   : 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]]
-  ? [[|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]]
   : Computational method for identifying energetically favorable binding sites on biological molecules  [[tutorials:tutorials|Tutorial]]
@@ Line 54: / Line 41: @@
 ==== Not updated software ====
+  ? [[http://projects.h-its.org/mcm/software/amber.html|AMBER patches]]
+  : 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]]
   : Database of Simulated Molecular Motions
@@ Line 64: / Line 55: @@
   ? [[http://projects.h-its.org/mcm/software/pka|pka calculation]]
   : Scripts for pKa calculations with UHBD
+===== References =====

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