@article{nokey,

title = {Contact-Map-Driven Exploration of Heterogeneous Protein-Folding Paths},

author = {Ziad Fakhoury, Gabriele C. Sosso, Scott Habershon},

url = {https://sossogroup.uk/wp-content/uploads/2024/09/fakhoury-et-al-2024-contact-map-driven-exploration-of-heterogeneous-protein-folding-paths.pdf},

doi = {10.1021/acs.jctc.4c00878},

year  = {2024},

date = {2024-09-04},

urldate = {2024-09-04},

journal = {Journal of Computational and Theoretical Chemistry},

abstract = {We have recently shown how physically realizable protein-folding pathways can be generated using directed walks in the space of inter-residue contact-maps; combined with a back-transformation to move from protein contact-maps to Cartesian coordinates, we have demonstrated how this approach can generate protein-folding trajectory ensembles without recourse to molecular dynamics. In this article, we demonstrate that this framework can be used to study a challenging protein-folding problem that is known to exhibit two different folding paths which were previously identified through molecular dynamics simulation at several different temperatures. From the viewpoint of protein-folding mechanism prediction, this particular problem is extremely challenging to address, specifically involving folding to an identical nontrivial compact native structure along distinct pathways defined by heterogeneous secondary structural elements. Here, we show how our previously reported contact-map-based protein-folding strategy can be significantly enhanced to enable accurate and robust prediction of heterogeneous folding paths by (i) introducing a novel topologically informed metric for comparing two protein contact maps, (ii) reformulating our graph-represented folding path generation, and (iii) introducing a new and more reliable structural back-mapping algorithm. These changes improve the reliability of generating structurally sound folding intermediates and dramatically decrease the number of physically irrelevant folding intermediates generated by our previous simulation strategy. Most importantly, we demonstrate how our enhanced folding algorithm can successfully identify the alternative folding mechanisms of a multifolding-pathway protein, in line with direct molecular dynamics simulations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Unravelling  the  Interactions  Between  Small  Molecules  and  Liposomal Bilayers via Molecular Dynamics and  Thermodynamic Modelling},

author = {Christopher M. Miles, Shane Cullen, Hussein Kenaan, Wenjie Gu, Gavin P. Andrews, Gabriele C. Sosso, Yiwei Tian},

url = {https://sossogroup.uk/wp-content/uploads/2024/07/Text-2.pdf},

doi = {https://doi.org/10.1016/j.ijpharm.2024.124367},

year  = {2024},

date = {2024-06-17},

urldate = {2024-06-17},

journal = {International Journal of Pharmaceutics},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Blow2023Ammonium,

title = {Understanding the impact of ammonium ion substitions on heterogeneous ice nucleation},

author = {KE Blow and TF Whale and D Quigley and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2023/07/Blow2023Ammonium.pdf},

doi = {10.1039/D3FD00097D},

year  = {2023},

date = {2023-09-26},

urldate = {2023-09-26},

journal = {Faraday Discussions},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Barnard2023Stability,

title = {Combining machine learning and molecular simulations to predict the stability of amorphous drugs},

author = {T Barnard and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2023/09/Barnard2023Stability.pdf},

doi = {10.1063/5.0156222},

year  = {2023},

date = {2023-06-08},

journal = {The Journal of Chemical Physics},

volume = {159},

number = {1},

pages = {014503},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Blow2023Interplayb,

title = {Interplay of multiple clusters and initial interface positioning for forward flux sampling simulations of crystal nucleation},

author = {KE Blow and GA Tribello and GC Sosso and D Quigley},

url = {https://sossogroup.uk/wp-content/uploads/2023/06/Blow2023FFSInterfaces.pdf},

doi = {10.1063/5.0152343},

year  = {2023},

date = {2023-06-01},

journal = {The Journal of Chemical Physics},

volume = {158},

number = {22},

pages = {224102},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fkhoury2023ProteinFolding,

title = {Generating protein folding trajectories using contact-map-driven directed walks},

author = {Z Fakhoury and GC Sosso and S Habershon},

url = {https://sossogroup.uk/wp-content/uploads/2023/04/Fakhoury2023ProteinFolding.pdf},

doi = {10.1021/acs.jcim.3c00023},

year  = {2023},

date = {2023-04-03},

urldate = {2023-04-03},

journal = {Journal of Chemical Information and Modeling},

volume = {63},

number = {7},

pages = {2181--2195},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gonzalez-Jimenez2023Boson,

title = {Understanding the emergence of the boson peak in molecular glasses},

author = {M González-Jiménez and T Barnard and BA Russell and NV Tukachev and U Javornik and L-A Hayes and AJ Farrell and S Guinane and HM Senn and AJ Smith and M Wilding and G Mali and M Nakano and Y Miyazaki and P McMillan and GC Sosso and K Wynne},

url = {https://sossogroup.uk/wp-content/uploads/2023/01/Gonzalez-Jimenez2023Boson.pdf},

doi = {10.1038/s41467-023-35878-6},

year  = {2023},

date = {2023-01-13},

urldate = {2023-01-13},

journal = {Nature Communications},

volume = {14},

number = {1},

pages = {1--11},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barnard2022GAPredictive,

title = {Leveraging genetic algorithms to maximise the predictive capabilities of the SOAP descriptor},

author = {T Barnard and S Tseng and JP Darby and AP Bartók and A Broo and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2022/11/Barnard2022GAPredictive.pdf},

doi = {10.1039/d2me00149g},

year  = {2022},

date = {2022-11-03},

urldate = {2022-11-23},

journal = {Molecular Systems Design & Engineering},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Warren2022Minimalisticb,

title = {Minimalistic ice recrystallisation inhibitors based on phenylalanine},

author = {MT Warren and I Galpin and M Hasan and SA Hindmarsh and JD Padrnos and C Edwards-Gayle and RT Mathers and DJ Adams and GC Sosso and MI Gibson },

url = {https://sossogroup.uk/wp-content/uploads/2022/06/Warren2022Minimalistic.pdf},

doi = {10.1039/D2CC02531K},

year  = {2022},

date = {2022-08-20},

urldate = {2022-08-20},

journal = {Chemical Communications},

volume = {58},

number = {55},

pages = {7658--7661},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sosso2022Structural,

title = {The role of structural order in heterogeneous ice nucleation},

author = {GC Sosso and Sudera P and AT Backes and TF Whale and J Fröhlich-Nowoisky and M Bonn and A Michaelides and EHG Backus},

url = {https://sossogroup.uk/wp-content/uploads/2022/04/StructuralOrderIceNucleation.pdf},

doi = {10.1039/D1SC06338C},

year  = {2022},

date = {2022-04-08},

journal = {Chemical Science},

volume = {13},

issue = {17},

pages = {5014-5026},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Warren22IRI,

title = {Ice recrystallization inhibition by amino acids: the curious case of alpha- and beta-alanine},

author = {MT Warren and I Galpin and F Bachtiger and MI Gibson and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2022/03/IRIbyAminoAcidsWarren.pdf},

doi = {10.1021/acs.jpclett.1c04080},

year  = {2022},

date = {2022-03-03},

journal = {The Journal of Physical Chemistry Letters},

volume = {13},

number = {9},

pages = {2237-2244},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Miles22Lipid,

title = {Lipid bilayers as potential ice nucleating agents},

author = {CM Miles and P-C Hsu and AM Dixon and S Khalid and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2022/03/lipid_bilayers_as_potential_ice_nucleating_agents.pdf},

doi = {10.1039/D1CP05465A},

year  = {2022},

date = {2022-03-01},

urldate = {2022-03-01},

journal = {Physical Chemistry Chemical Physics},

volume = {24},

issue = {11},

pages = {6476-6491},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gasparotto22Interfaces,

title = {How do interfaces alter the dynamics of supercooled water?},

author = {P Gasparotto and M Fitzner and SJ Cox and GC Sosso and A Michaelides},

url = {https://sossogroup.uk/wp-content/uploads/2022/03/HowdoInterfactesAlterDynamicsofSupercooledWater.pdf},

doi = {10.1039/D2NR00387B},

year  = {2022},

date = {2022-02-28},

journal = {Nanoscale},

volume = {14},

issue = {11},

pages = {4254-4262},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Herlihy21Recovering,

title = {Recovering local structure information from high-pressure total scattering experiments},

author = {A Herlihy and HS Geddes and GC Sosso and CL Bull and CK Ridley and AL Goodwin and MS Senn and NP Funnell},

url = {https://sossogroup.uk/wp-content/uploads/2021/12/kc5131.pdf},

doi = {10.1107/S1600576721009420},

year  = {2021},

date = {2021-09-09},

urldate = {2021-09-09},

journal = {Journal of Applied Crystallography},

volume = {54},

number = {6},

pages = {1546-1554},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Blow2021Nucleation,

title = {The seven deadly sins: When computing crystal nucleation rates, the devil is in the details},

author = {KE Blow and D Quigley and GC Sosso },

url = {https://sossogroup.uk/wp-content/uploads/2021/07/Blow2021Nucelation.pdf},

doi = {10.1063/5.0055248},

year  = {2021},

date = {2021-07-22},

journal = {The Journal of Chemical Physics},

volume = {155},

number = {4},

pages = {040901},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stevens2021Minimalistic,

title = {A minimalistic cyclic ice-binding peptide from phage display},

author = {CA Stevens and F Bachtiger and X-D Kong and LA Abriata and GC Sosso and MI Gibson and H-A Klok},

url = {https://sossogroup.uk/wp-content/uploads/2021/05/s41467-021-22883-w.pdf},

doi = {0.1038/s41467-021-22883-w},

year  = {2021},

date = {2021-05-11},

journal = {Nature Communications},

volume = {12},

pages = {2675},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wang2021Kinetics,

title = {Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries},

author = {L Wang and J Chen and SJ Cox and L Liu and GC Sosso and N Li and P Gao and A Michaelides and E Wang and X Bai},

url = {https://sossogroup.uk/wp-content/uploads/2021/05/PhysRevLett.126.136001.pdf},

doi = {10.1103/PhysRevLett.126.136001},

year  = {2021},

date = {2021-03-29},

journal = {Physical Review Letters},

volume = {126},

number = {13},

pages = {136001},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mistry2021Modelling,

title = {Modelling the interactions and diffusion of NO in amorphous SiO2},

author = {MV Mistry and J Cottom and K Patel and AL Shluger and GC Sosso and G Pobegen},

url = {https://sossogroup.uk/wp-content/uploads/2021/01/NO_in_amorphous_SiO2.pdf},

doi = {10.1088/1361-651X/abdc69},

year  = {2021},

date = {2021-03-11},

journal = {Modelling and Simulation in Materials Science and Engineering},

volume = {29},

number = {3},

pages = {035008},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bachtiger2021PVA,

title = {The atomistic details of the ice recrystallisation inhibition activity of PVA.},

author = {F Bachtiger and TR Congdon and C Stubbs and MI Gibson and GC Sosso},

url = {https://sossogroup.uk/wp-content/uploads/2021/03/AtomisticPVASosso.pdf},

doi = {0.1038/s41467-021-21717-z},

year  = {2021},

date = {2021-02-26},

journal = {Nature Communications},

volume = {12},

number = {1323},

keywords = {},

pubstate = {published},

tppubtype = {article}

}