The list of publications below have directly benefitted from the resources that HECBioSim provides.

 

Publications citing current grant code (EP/R029407/1)

Structural Basis for Substrate Specificity and Regulation of Nucleotide Sugar Transporters in the Lipid Bilayer - Nature Communications - 11/10/2019
Joanne L. Parker, Robin A. Corey, Phillip J. Stansfeld, Simon Newstead

The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus - Frontiers in Molecular Biosciences - 01/10/2019
Havva Yalinca, Charlotte Julie Caroline Gehin, Vladimiras Oleinikovas, Hilal A. Lashuel, Francesco Luigi Gervasio, Annalisa Pastore

The Morphogen Sonic Hedgehog Inhibits its Receptor Patched by a Pincer Grasp Mechanism - Nature Chemical Biology - 23/09/19
Amalie F. Rudolf, Maia Kinnebrew, Christiane Kowatsch, T. Bertie Ansell, Kamel El Omari, Benjamin Bishop, Els Pardon, Rebekka A. Schwab, Tomas Malinauskas, Mingxing Qian, Ramona Duman, Douglas F. Covey, Jan Steyaert, Armin Wagner, Mark S. P. Sansom, Rajat Rohatgi & Christian Siebold

Sharing Data from Molecular Simulations - Journal of Chemical Information and Modeling - 17/09/2019
Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M.J.J. Bonvin, Matthieu Chavent, John Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, O. H. Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K.S. Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov

The Structural Basis of Lipid Scrambling and Inactivation in the Endoplasmic Reticulum Scramblase TMEM16K - Nature Communications - 02/09/2019
Simon R. Bushell, Ashley C. W. Pike, Maria E. Falzone, Nils J. G. Rorsman, Chau M. Ta, Robin A. Corey, Thomas D. Newport, John C. Christianson, Lara F. Scofano, Chitra A. Shintre, Annamaria Tessitore, Amy Chu, Qinrui Wang, Leela Shrestha, Shubhashish M. M. Mukhopadhyay, James D. Love, Nicola A. Burgess-Brown, Rebecca Sitsapesan, Phillip J. Stansfeld, Juha T. Huiskonen, Paolo Tammaro, Alessio Accardi, Elisabeth P. Carpenter

Insights into Membrane Protein–Lipid Interactions from Free Energy Calculations - Journal of Chemical Theory and Computation - 02/09/2019
Robin A. Corey, Owen N. Vickery, Mark S. P. Sansom, Phillip J. Stansfeld

Membrane Recognition and Binding by the Phosphatidylinositol Phosphate Kinase PIP5K1A: A Multiscale Simulation Study - Structure - 06/08/2019
Sarah-Beth T.A. Amos, Antreas C. Kalli, JiyeShi, Mark S.P.Sansom

Structure and Functional Analysis of the Legionella Chitinase ChiA Reveals a Novel Mechanism of Metal-Dependent Mucin Degradation - bioRxiv - 02/07/2019
Katherine H. Richardson, Lubov S. Grigoryeva, Paula Corsini, Richard C. White, Rosie Shaw, Theo J. Portlock, Benjamin Dorgan, Arianna Fornili, Nicholas P. Cianciotto, James A. Garnett

A Heuristic Derived from Analysis of the Ion Channel Structural Proteome Permits the Rapid Identification of Hydrophobic Gates - PNAS - 24/06/2019
Shanlin Rao, Gianni Klesse, Phillip J. Stansfeld, Stephen J. Tucker, Mark S. P. Sansom

The Dual Role of Histidine as General Base and Recruiter of a Third Metal Ion in HIV-1 RNase H - Chemrxiv - 13/06/2019
Simon L. Dürr, Olga Bohuszewicz, Reynier Suardiaz, Pablo G. Jambrina, Christine Peter, Yihan Shao, Edina Rosta

A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations  - Biorxiv - 12/06/2019
Marc A. Dämgen, Philip C. Biggin

Understanding Ligand Binding Selectivity in a Prototypical GPCR Family - Journal of Chemical Information and Modeling - 24/05/2019
Giulio Mattedi, Francesca Deflorian, Jonathan S. Mason, Chris de Graaf, Francesco L. Gervasio

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor - The Journal of Physical Chemistry Letters - 01/04/2019
Antonija Kuzmanic, Ruth B. Pritchard, D. Flemming Hansen, Francesco L. Gervasio

The Molecular Basis for an Allosteric Inhibition of K+-flux Gating in K2P Channels - eLife - 26/02/2019
Susanne Rinné, Aytug K Kiper, Kirsty S Vowinkel, David Ramírez, Marcus Schewe, Mauricio Bedoya, Diana Aser, Isabella Gensler, Michael F Netter, Phillip J Stansfeld, Thomas Baukrowitz, Wendy Gonzalez, Niels Decher

A Lipid Gating Mechanism for the Channel-Forming O Antigen ABC Transporter - Nature Communications - 18/02/2019
Christopher A. Caffalette, Robin A. Corey, Mark S. P. Sansom, Phillip J. Stansfeld, Jochen Zimmer

CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space - Journal of Chemical Theory and Computation - 08/01/2019
Ardita Shkurti, Ioanna Danai Styliari, Vivek Balasubramanian, Iain Bethune, Conrado Pedebos, Shantenu Jha, Charles A. Laughton

Binding Pockets in Proteins Induced by Mechanical Stress - Journal of Chemical Theory and Computation - 10/12/2018
Matteo Tiberti, Bob-Dan Lechner, Arianna Fornili

Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor - Biomolecular Simulations in Structure‐Based Drug Discovery - 10/12/2018
Federico Comitani, Francesco L. Gervasio

Defining an Optimal Metric for the Path Collective Variables - Journal of Chemical Theory and Computation - 23/11/2018
Ladislav Hovan, Federico Comitani, Francesco L. Gervasio

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions - Nucleic Acids Research - 12/11/2018
Thomas D. Newport, Mark S. P. Samsom, Phillip J. Stansfeld

In Silico Screening for Solid Dispersions: The Trouble with Solubility Parameters and χFH - Molecular Pharmaceutics - 24/08/2018
Eleanor R. Turpin, Vincenzo Taresco, Wathiq A. Al-Hachami, Jonathan Booth, Kevin Treacher, Simone Tomasi, Cameron Alexander, Jonathan Burley, Charles A. Laughton, Martin C. Garnett