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projects:data [2013/10/30 12:18]
richter [MCM supplemental data]
projects:data [2018/03/12 13:59] (current)
richter [MCM supplemental data]
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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
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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}} |
  
-  *   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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 +  *   ​[[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]]. ​
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-  * 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}}|. 
  
 +  * [[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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