MCM supplemental data

Note: For most recent publications, supplemental data is made available in the publication and on https://zenodo.org/Zenodo at the link given in the respective paper. Some of our MD trajectories are available in MDDB – Molecular Dynamics Data Bank where they can be visualized and analyzed in a webbrowser. On this webpage, we list only additional supplemental data.

Supplemental data published before 2011 can be found in our archive.

In addition, our Ubiquitin and Ubiquitin-like Protein Web Resource has data from "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.

Supplemental data relating to papers published in or after 2011 can be found below:

In addition, KBbox contains sets of data on protein-drug binding kinetics and information on computational methods for studying the kinetics of molecular binding, including tutorials. "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.

• 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.: PDB files for the encounter complexes (zipped)

• For simulation of the cysteine synthase complex ( 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:
    • Coenzyme A (CoA): lib, parm
    • Pyridoxal 5′-phosphate covalently bound to a lysine residue (K-PLP): lib, parm
  • For PDB coordinates, see Supplementary material.

• 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 : PDB files for models (zipped).

• 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 : PDB files for MAP-ribosome encounter complexes (zipped (bzip2) tar file).

• 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 : Movie of diffusion of a solution of hemoglobin tetramers at a 0.11 volume fraction simulated with the SDA software (zipped (zip) file).

• 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 : 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).

• 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

• 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 : PDB coordinates of model deposited in ModelArchive doi: 10.5452/ma-ww4oz

• 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 | Accepted manuscript

• 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 | Submitted manuscript

• Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics ; M. Glaser, N. J. Bruce, S. B. Han, R. C. Wade, J Phys Chem B. 2021 May 13;125(18):4654-4666 (https://pubs.acs.org/doi/10.1021/acs.jpcb.1c00902) Script used can be found here