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Recent Publications from the Theory Research Interest Group

Large scale parallelization in stochastic coupled cluster.
JS Spencer, VA Neufeld, WA Vigor, RST Franklin, AJW Thom
– The Journal of chemical physics
(2018)
149,
204103
(DOI: 10.1063/1.5047420)
Empirical estimation of permutation-based metabolome-wide significance thresholds
A Peluso, T Ebbels, R Glen
(2018)
(DOI: 10.1101/478370)
Lattice models and Monte Carlo methods for simulating DNA origami self-assembly
A Cumberworth, A Reinhardt, D Frenkel
– Journal of Chemical Physics
Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs
HR Noori, LH Mervin, V Bokharaie, Ö Durmus, L Egenrieder, S Fritze, B Gruhlke, G Reinhardt, H-H Schabel, S Staudenmaier, NK Logothetis, A Bender, R Spanagel
– Nature communications
(2018)
9,
4699
(DOI: 10.1038/s41467-018-07239-1)
Mapping Surface Hydrophobicity of α-Synuclein Oligomers at the Nanoscale
J-E Lee, JC Sang, M Rodrigues, AR Carr, MH Horrocks, S De, MN Bongiovanni, P Flagmeier, CM Dobson, DJ Wales, SF Lee, D Klenerman
– Nano Lett
(2018)
(DOI: 10.1021/acs.nanolett.8b02916)
Erratum: Discovery of a non-toxic [1,2,4]triazolo[1,5-a]pyrimidin-7-one (WS-10) that modulates ABCB1-mediated multidrug resistance (MDR) (Bioorganic & medicinal chemistry (2018) 26 18 (5006-5017) PII: S0968-0896(18)31826-1)
L Chang, M Xiao, L Yang, S Wang, S-Q Wang, A Bender, A Hu, Z-S Chen, B Yu, H-M Liu
– Bioorganic & medicinal chemistry
(2018)
26,
5974
(DOI: 10.1016/j.bmc.2018.10.027)
Mutational Basin-Hopping – Combined Structure and Sequence Optimisation for Biomolecules
K Röder, DJ Wales
– J Phys Chem Lett
(2018)
9,
6169
(DOI: 10.1021/acs.jpclett.8b02839)
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Prediction Errors for Deep Neural Networks
I Cortés-Ciriano, A Bender
– J Chem Inf Model
(2018)
(DOI: 10.1021/acs.jcim.8b00542)
Analysis of the Ub to Ub-CR transition in ubiquitin
K Röder, DJ Wales
– Biochemistry
(2018)
57,
6180
(DOI: 10.1021/acs.biochem.8b00770)
Topological Ring-Currents and Clar Sextets in Fully Benzenoid Hydrocarbons. II. Large Structures Containing More than 18 Rings
TK Dickens, RB Mallion
– The journal of physical chemistry. A
(2018)
122,
8865
(DOI: 10.1021/acs.jpca.8b08723)
Topological Ring-Currents and Clar Sextets in Fully Benzenoid Hydrocarbons I. Structures with Fewer than 18 Rings.
TK Dickens, RB Mallion
– J Phys Chem A
(2018)
122,
8858
(DOI: 10.1021/acs.jpca.8b08722)
Information-Derived Mechanistic Hypotheses for Structural Cardiotoxicity
F Svensson, A Zoufir, S Mahmoud, AM Afzal, I Smit, KA Giblin, PJ Clements, JT Mettetal, A Pointon, JS Harvey, N Greene, RV Williams, A Bender
– Chemical research in toxicology
(2018)
31,
1119
(DOI: 10.1021/acs.chemrestox.8b00159)
Co-localization features for classification of tumors using mass spectrometry imaging
P Inglese, G dos Santos Correia, P Pruski, R Glen, Z Takats
(2018)
(DOI: 10.1101/440057)
Discovery of a small-molecule inhibitor of specific serine residue BAD phosphorylation.
V Pandey, B Wang, CD Mohan, AR Raquib, S Rangappa, V Srinivasa, JE Fuchs, KS Girish, T Zhu, A Bender, L Ma, Z Yin, Basappa, KS Rangappa, PE Lobie
– Proceedings of the National Academy of Sciences of the United States of America
(2018)
115,
E10505
(DOI: 10.1073/pnas.1804897115)
Correlation energies of the high-density spin-polarized electron gas to meV accuracy
M Ruggeri, PL Rios, A Alavi
– Physical Review B - Condensed Matter and Materials Physics
(2018)
98,
ARTN 161105
(DOI: 10.1103/PhysRevB.98.161105)
Prospectively Validated Proteochemometric Models for the Prediction of Small Molecule Binding to Bromodomain Proteins
KA Giblin, SJ Hughes, H Boyd, P Hansson, A Bender
– Journal of Chemical Information and Modeling
(2018)
58,
1870
(DOI: 10.1021/acs.jcim.8b00400)
Effects of random pinning on the potential energy landscape of a supercooled liquid
SP Niblett, VK de Souza, RL Jack, DJ Wales
– Journal of Chemical Physics
(2018)
149,
114503
(DOI: 10.1063/1.5042140)
Finite electric displacement simulations of polar ionic solid-electrolyte interfaces: Application to NaCl(111)/aqueous NaCl solution
T Sayer, M Sprik, C Zhang
– arXiv
Terahertz VRT Spectroscopy of the Water Hexamer-h12 Cage: Dramatic Libration-Induced Enhancement of Hydrogen Bond Tunneling Dynamics
WTS Cole, Ö Yönder, AA Sheikh, RS Fellers, MR Viant, RJ Saykally, JD Farrell, DJ Wales
– Journal of Physical Chemistry A
(2018)
122,
7421
(DOI: 10.1021/acs.jpca.8b05777)
Proline provides site-specific flexibility for in vivo collagen
WY Chow, CJ Forman, D Bihan, AM Puszkarska, R Rajan, DG Reid, DA Slatter, LJ Colwell, DJ Wales, RW Farndale, MJ Duer
– Scientific reports
(2018)
8,
13809
(DOI: 10.1038/s41598-018-31937-x)

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