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projects:data [2013/10/30 11:05] richter [MCM supplemental data] |
projects:data [2018/03/12 13:59] 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 | ||
| + | ^ 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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| + | * [[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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| - | * 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)}} | ||
| * 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)}}. | ||
