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projects:data [2013/10/30 11:05] richter [MCM supplemental data] |
projects:data [2021/07/08 20:55] wade |
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====== MCM supplemental data ====== | ====== MCM supplemental data ====== | ||
- | **Supplemental data published before 2011** can be found in [[http://mcm.h-its.org/archive/data|our archive]]. | + | **Supplemental data published before 2011** can be found in [[https://projects.h-its.org/mcm/data/|our archive]]. |
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+ | 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: | ||
- | * On the structure and dynamics of the complex of the nucleosome and the linker histone, Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade. Nucl. Acid. Res., (2011) 1:9.: {{:projects:pdb_nar.zip|PDB files for the encounter complexes (zipped)}} | + | 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. |
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+ | * [[http://nar.oxfordjournals.org/content/39/12/5255.long | On the structure and dynamics of the complex of the nucleosome and the linker histone]], Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade. Nucl. Acid. Res., (2011) 1:9.: {{:projects:pdb_nar.zip|PDB files for the encounter complexes (zipped)}} | ||
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* For simulation of the cysteine synthase complex ([[http://www.ncbi.nlm.nih.gov/pubmed/18801369?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum | A mechanistic model of the cysteine synthase complex]], Feldman-Salit et al, J Mol Biol. 2009 Feb 13;386(1):37-59): | * For simulation of the cysteine synthase complex ([[http://www.ncbi.nlm.nih.gov/pubmed/18801369?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum | A mechanistic model of the cysteine synthase complex]], Feldman-Salit et al, J Mol Biol. 2009 Feb 13;386(1):37-59): | ||
* Parameters derived using Antechamber for simulations with AMBER8 using parm99.dat and gaff.dat: | * Parameters derived using Antechamber for simulations with AMBER8 using parm99.dat and gaff.dat: | ||
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* Pyridoxal 5′-phosphate covalently bound to a lysine residue (K-PLP): {{:projects:llp.lib.txt|lib}}, {{:projects:llp-new.parm.txt|parm}} | * Pyridoxal 5′-phosphate covalently bound to a lysine residue (K-PLP): {{:projects:llp.lib.txt|lib}}, {{:projects:llp-new.parm.txt|parm}} | ||
* For PDB coordinates, see [[http://mcm.h-its.org/archive/data/cysteine-synthase/ | Supplementary material]]. | * For PDB coordinates, see [[http://mcm.h-its.org/archive/data/cysteine-synthase/ | Supplementary material]]. | ||
- | * Related PDB files for: Nat Struct Mol Biol. 2012 Dec;19(12):1338-46. doi: 10.1038/nsmb.2441. Epub 2012 Nov 18. A tightly regulated molecular toggle controls AAA+ disaggregase. Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B. can be found {{{{:projects:clpb_si-b.zip|here}}|. | ||
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+ | * [[http://www.ncbi.nlm.nih.gov/pubmed/23160353 | A tightly regulated molecular toggle controls AAA+ disaggregase]], Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B., Nat Struct Mol Biol. (2012) 19:1338-46. doi: 10.1038/nsmb.2441 : {{:projects:clpb_si-c.zip|PDB files for models (zipped)}}. | ||
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+ | * [[http://www.ncbi.nlm.nih.gov/pubmed/23770820 | Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding]], Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G, Nat Struct Mol Biol. (2013) 20:843-50. doi: 10.1038/nsmb.2615 : {{:projects:nsmb_kramer_2013_dockingresults.tar.bz2| PDB files for MAP-ribosome encounter complexes (zipped (bzip2) tar file)}}. | ||
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+ | * [[http://pubs.acs.org/doi/abs/10.1021/jp212532h | Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions]], Mereghetti P, Wade, RC, J. Phys. Chem. B. (2012) 116:8523-8533. doi: 10.1021/jp212532h : {{:projects:hemoglobin_0.11_136frames.zip| Movie of diffusion of a solution of hemoglobin tetramers at a 0.11 volume fraction simulated with the SDA software (zipped (zip) file)}}. | ||
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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)}}. | ||
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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 | ||
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+ | ^ 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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+ | * [[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 | ||
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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 |Accepted manuscript}} | ||
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+ | * 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., in press, DOI: 10.1016/j.chembiol.2021.01.003 | [[http://dx.doi.org/10.2139/ssrn.3656604 |Submitted manuscript]] | ||
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