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Recent Publications from the Theory Research Interest Group

Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction
MC Robinson, RC Glen, AA Lee
– Journal of computer-aided molecular design
(2020)
34,
717
(DOI: 10.1007/s10822-019-00274-0)
Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids.
N Koundouros, E Karali, A Tripp, A Valle, P Inglese, NJS Perry, DJ Magee, S Anjomani Virmouni, GA Elder, AL Tyson, ML Dória, A van Weverwijk, RF Soares, CM Isacke, JK Nicholson, RC Glen, Z Takats, G Poulogiannis
– Cell
(2020)
181,
1596
(DOI: 10.1016/j.cell.2020.05.053)
Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components.
JR Espinosa, JA Joseph, I Sanchez-Burgos, A Garaizar, D Frenkel, R Collepardo-Guevara
– Proceedings of the National Academy of Sciences
(2020)
117,
13238
(DOI: 10.1073/pnas.1917569117)
QSAR-derived affinity fingerprints (part 1): Fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping
C Škuta, I Cortés-Ciriano, W Dehaen, P Kříž, GJP Van Westen, IV Tetko, A Bender, D Svozil
– Journal of Cheminformatics
(2020)
12,
39
(DOI: 10.1186/s13321-020-00443-6)
Predicting the phase diagram of titanium dioxide with random search and pattern recognition
A Reinhardt, CJ Pickard, B Cheng
– Physical chemistry chemical physics : PCCP
(2020)
22,
12697
(DOI: 10.1039/d0cp02513e)
Band positions of anatase (001) and (101) surfaces in contact with water from density functional theory
J Geiger, M Sprik, MM May
– The Journal of Chemical Physics
(2020)
152,
194706
(DOI: 10.1063/5.0004779)
The Lennard-Jones potential: when (not) to use it
X Wang, S Ramírez-Hinestrosa, J Dobnikar, D Frenkel
– Physical chemistry chemical physics : PCCP
(2020)
22,
10624
(DOI: 10.1039/c9cp05445f)
Numerical calculation of free-energy barriers for entangled polymer nucleation.
X Tang, F Tian, T Xu, L Li, A Reinhardt
– The Journal of chemical physics
(2020)
152,
224904
(DOI: 10.1063/5.0009716)
Periodicity of Single-Molecule Magnet Behaviour of Heterotetranuclear Lanthanide Complexes across the Lanthanide Series: A Compendium
DC Izuogu, T Yoshida, G Cosquer, JN Asegbeloyin, H Zhang, AJW Thom, M Yamashita
– Chemistry - A European Journal
(2020)
26,
6036
(DOI: 10.1002/chem.202000161)
Reactive momentum transfer contributes to the self propulsion of Janus particles
S Eloul, WCK Poon, O Farago, D Frenkel
– Physical Review Letters
(2020)
124,
188001
(DOI: 10.1103/physrevlett.124.188001)
Affinity-Selected Bicyclic Peptide G-Quadruplex Ligands Mimic a Protein-like Binding Mechanism
KC Liu, K Röder, C Mayer, S Adhikari, DJ Wales, S Balasubramanian
– J Am Chem Soc
(2020)
142,
8367
(DOI: 10.1021/jacs.0c01879)
Energy Landscapes of Deoxyxylo- A nd Xylo-Nucleic Acid Octamers
DJ Sharpe, K Röder, DJ Wales
– J Phys Chem B
(2020)
124,
4062
(DOI: 10.1021/acs.jpcb.0c01420)
Reactive Momentum Transfer Contributes to the Self-Propulsion of Janus Particles
S Eloul, WCK Poon, O Farago, D Frenkel
– Physical review letters
(2020)
124,
188001
(DOI: 10.1103/physrevlett.124.188001)
Dynamical phase coexistence in the Fredrickson-Andersen model
RL Jack, T Nemoto, V Lecomte
– Journal of Statistical Mechanics Theory and Experiment
(2020)
2020,
053204
(DOI: 10.1088/1742-5468/ab7af6)
EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks.
H Bashiri, H Rahmani, V Bashiri, D Módos, A Bender
– Comput Biol Med
(2020)
120,
103740
(DOI: 10.1016/j.compbiomed.2020.103740)
Studying polymer diffusiophoresis with Non-Equilibrium Molecular Dynamics
S Ramírez-Hinestrosa, H Yoshida, L Bocquet, D Frenkel
– J Chem Phys
(2020)
152,
164901
(DOI: 10.1063/5.0007235)
From sticky-hard-sphere to Lennard-Jones-type clusters
L Trombach, RS Hoy, DJ Wales, P Schwerdtfeger
– Physical review. E
(2020)
97,
043309
(DOI: 10.1103/PhysRevE.97.043309)
Effect of the interaction strength and anisotropy on the diffusio-phoresis of spherical colloids
J Wei, S Ramírez-Hinestrosa, J Dobnikar, D Frenkel
– Soft Matter
(2020)
16,
3621
(DOI: 10.1039/c9sm02053e)
Assessing the structural heterogeneity of supercooled liquids through community inference.
J Paret, RL Jack, D Coslovich
– The Journal of chemical physics
(2020)
152,
144502
(DOI: 10.1063/5.0004732)
Defining, Calculating, and Converging Observables of a Kinetic Transition Network
TD Swinburne, DJ Wales
– Journal of Chemical Theory and Computation
(2020)
16,
2661
(DOI: 10.1021/acs.jctc.9b01211)

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