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--- projects:data [2018/03/12 13:59] – [MCM supplemental data] richter
+++ projects:data [2026/06/18 09:53] (current) – wade
@@ Line 2: / Line 2: @@
 ====== MCM supplemental data ======
-**Supplemental data published before 2011** can be found in [[http://mcm.h-its.org/archive/data|our archive]].
+**Note:** For most recent publications, supplemental data is made available in the publication and on [[https://zenodo.org/Zenodo]] at the link given in the respective paper. Some of our MD trajectories are available in [[https://irb-dev.mddbr.eu/#/browse?search=wade|MDDB – Molecular Dynamics Data Bank]] where they can be visualized and analyzed in a webbrowser.  On this webpage, we list only additional supplemental data.
-**Supplemental data relating to papers published in or after 2011** can be found below:
+**Supplemental data published before 2011** can be found in [[https://projects.h-its.org/mcm/data/|our archive]].
+In addition,  our [[http://www.ubiquitin-resource.org/|Ubiquitin and Ubiquitin-like Protein Web Resource]] has data from [[https://doi.org/10.1016/j.str.2004.06.017|"Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family"]], Winn PJ, Religa TL, Battey JND, Banerjee A, Wade RC, Structure (2004) 12(9):1563-74.
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-  *  [[http://onlinelibrary.wiley.com/doi/10.1002/prot.25167/abstract|Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties.]] Rudi Tong, Rebecca C. Wade and Neil J. Bruce (2016), Proteins: Struct. Func. Bioinf., 84, 1844-1858. DOI: 10.1002/prot.25167
+**Supplemental data relating to papers published in or after 2011** can be found below:
-^  Structures   ^    Grids    ^
-|{{ :projects:modelledisoformstructuresnorefine.tgz |Unrefined modelled AC isoforms for small molecule analysis}} |{{ :projects:electrostaticgridsnorefine.tgz |Electrostatic potential grids from unrefined structures, UHBD format}} |
+In addition,  [[https://kbbox.h-its.org/toolbox/|KBbox]] contains sets of data on protein-drug binding kinetics and information on computational methods for studying the kinetics of molecular binding, including tutorials.   [[https://doi.org/10.1021/acs.jcim.9b00485|"KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding"]], Bruce NJ, Ganotra GK, Richter S, Wade RC, J. Chem. Inf. Model. (2019) 59, 3630-3634.
-|{{ :projects:modelledisoformstructures.tgz |Modelled AC isoforms}}  |{{ :projects:electrostaticgrids.tgz |Electrostatic potential grids, UHBD format}} |
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@@ Line 40: / Line 42: @@
   * [[http://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/C6CP0020 | Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations]],  Ozboyaci M, Kokh DB, Wade, RC, Phys. Chem. Chem. Phys. (2016) 18:10191-10200. doi: 10.1039/C6CP00201C : {{:projects:blip-au_2orientations_perspective.zip| Movie showing adsorption of beta-lactamase inhibitor protein (BLIP) onto an Au(111) surface in molecular dynamics simulations starting from two encounter complexes generated by Brownian dynamics simulation. (zipped (zip) file)}}.
+----
+  *  [[http://onlinelibrary.wiley.com/doi/10.1002/prot.25167/abstract|Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties.]] Rudi Tong, Rebecca C. Wade and Neil J. Bruce (2016), Proteins: Struct. Func. Bioinf., 84, 1844-1858. DOI: 10.1002/prot.25167
+^  Structures   ^    Grids    ^
+|{{ :projects:modelledisoformstructuresnorefine.tgz |Unrefined modelled AC isoforms for small molecule analysis}} |{{ :projects:electrostaticgridsnorefine.tgz |Electrostatic potential grids from unrefined structures, UHBD format}} |
+|{{ :projects:modelledisoformstructures.tgz |Modelled AC isoforms}}  |{{ :projects:electrostaticgrids.tgz |Electrostatic potential grids, UHBD format}} |
+----
+  * [[https://doi.org/10.1002/1873-3468.13808 | Structural characterization of an Arf dimer interface: molecular mechanism of Arf‐dependent membrane scission ]], Diestelkoetter‐Bachert P, Beck R, Reckmann I, Hellwig A, Garcia‐Saez A, Zelman‐Hopf M, Hanke A, Alves AN, Wade RC, Mayer MP, Wieland F  FEBS Lett,(2020) 1873-3468.13808 doi:10.1002/1873-3468.13808 : [[https://modelarchive.org/doi/10.5452/ma-ww4oz | PDB coordinates of model deposited in ModelArchive]] doi: 10.5452/ma-ww4oz
+----
+  *  [[https://doi.org/10.1063/5.0019088 | A workflow for exploring ligand dissociation from a macromolecule]], Daria B Kokh, Bernd Doser, Stefan Richter, Fabian Ormersbach, Xingyi Cheng, Rebecca C Wade (2020), J.Chem.Phys., 153(12), 125102, DOI: 10.1063/5.0019088 | {{ :projects:jcp20-ar-clmd2020-02381.pdf |Accepted manuscript}}
+----
+  *  [[https://doi.org/10.2139/ssrn.3656604 | Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2]], Berger B, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schröder M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, Müller S, Frech M, Wade RC, Knapp S (2021), Cell Chem. Biol., S2451945621000039, DOI: 10.1016/j.chembiol.2021.01.003 | [[http://dx.doi.org/10.2139/ssrn.3656604 |Submitted manuscript]]
+----
+  * [[https://pubs.acs.org/doi/10.1021/acs.jpcb.1c00902| Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics ]]; M. Glaser, N. J. Bruce, S. B. Han, R. C. Wade, J Phys Chem B. 2021 May 13;125(18):4654-4666 (https://pubs.acs.org/doi/10.1021/acs.jpcb.1c00902) Script used can be found [[https://github.com/HITS-MCM/reweight_residue_secstruct|here]]

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