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--- projects:data [2013/10/30 12:19]
richter [MCM supplemental data]
+++ projects:data [2018/03/12 13:59] (current)
richter [MCM supplemental data]
@@ Line 6: / Line 6: @@
 **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)}}
+  *  [[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}} |
+----
+  *   [[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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@@ Line 19: / Line 28: @@
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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)}}.
 ----
+  * [[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)}}.
+----
+  * [[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)}}.
+----
+  * [[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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