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projects:data [2021/03/31 13:22]
wade [MCM supplemental data]
projects:data [2021/07/08 20:58] (current)
wade
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 **Supplemental data published before 2011** can be found in [[https://​projects.h-its.org/​mcm/​data/​|our archive]]. ​ **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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 **Supplemental data relating to papers published in or after 2011** can be found below: ​ **Supplemental data relating to papers published in or after 2011** can be found below: ​
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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 
  
- Structures ​  ​^ ​   Grids    ^ +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 bindingincluding tutorials. ​  ​[[https://doi.org/​10.1021/​acs.jcim.9b00485|"KBboxA Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding"​]],​ Bruce NJ, Ganotra GK, Richter S, Wade RC, JChem. Inf. Model. (2019) 593630-3634.
-|{{ :projects:​modelledisoformstructuresnorefine.tgz |Unrefined modelled AC isoforms for small molecule analysis}} |{{ :​projects:​electrostaticgridsnorefine.tgz |Electrostatic potential grids from unrefined structuresUHBD format}} | +
-|{{ :projects:modelledisoformstructures.tgz |Modelled AC isoforms}} ​ |{{ :projects:​electrostaticgrids.tgz |Electrostatic potential gridsUHBD format}} |+
  
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   * [[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://​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)}}.
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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
 +
 +^  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}} |
  
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-  *  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 |}} +  *  ​[[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}} 
  
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 +  *  [[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]] ​
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