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Department of Chemistry

 

Recent Publications from the Theory Research Interest Group

KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images.
I Cortes-Ciriano, A Bender
– Journal of Cheminformatics
(2019)
11,
41
(DOI: 10.1186/s13321-019-0364-5)
International Union of Basic and Clinical Pharmacology. CVII. Structure and Pharmacology of the Apelin Receptor with a Recommendation that Elabela/Toddler Is a Second Endogenous Peptide Ligand
C Read, D Nyimanu, TL Williams, DJ Huggins, P Sulentic, RGC Macrae, P Yang, RC Glen, JJ Maguire, AP Davenport
– Pharmacological reviews
(2019)
71,
467
(DOI: 10.1124/pr.119.017533)
OpenMolcas: From Source Code to Insight.
I Fdez Galván, M Vacher, A Alavi, C Angeli, F Aquilante, J Autschbach, JJ Bao, SI Bokarev, NA Bogdanov, RK Carlson, LF Chibotaru, J Creutzberg, N Dattani, MG Delcey, SS Dong, A Dreuw, L Freitag, LM Frutos, L Gagliardi, F Gendron, A Giussani, L González, G Grell, M Guo, CE Hoyer, M Johansson, S Keller, S Knecht, G Kovačević, E Källman, G Li Manni, M Lundberg, Y Ma, S Mai, JP Malhado, PÅ Malmqvist, P Marquetand, SA Mewes, J Norell, M Olivucci, M Oppel, QM Phung, K Pierloot, F Plasser, M Reiher, AM Sand, I Schapiro, P Sharma, CJ Stein, LK Sørensen, DG Truhlar, M Ugandi, L Ungur, A Valentini, S Vancoillie, V Veryazov, O Weser, TA Wesołowski, P-O Widmark, S Wouters, A Zech, JP Zobel, R Lindh
– Journal of chemical theory and computation
(2019)
acs.jctc.9b00532
(DOI: 10.1021/acs.jctc.9b00532)
Identifying mechanistically distinct pathways in kinetic transition networks
DJ Sharpe, DJ Wales
– The Journal of chemical physics
(2019)
151,
124101
(DOI: 10.1063/1.5111939)
Comparing theory and simulation for thermo-osmosis
K Proesmans, D Frenkel
– Journal of Chemical Physics
(2019)
151,
124109
(DOI: 10.1063/1.5123164)
Which quantum statistics-classical dynamics method is best for water?
RL Benson, G Trenins, SC Althorpe
– Faraday Discuss
(2019)
(DOI: 10.1039/C9FD00077A)
Understanding Conditional Associations between ToxCast in Vitro Readouts and the Hepatotoxicity of Compounds Using Rule-Based Methods.
SY Mahmoud, F Svensson, A Zoufir, D Módos, AM Afzal, A Bender
– Chemical research in toxicology
(2019)
acs.chemrestox.8b00382
(DOI: 10.1021/acs.chemrestox.8b00382)
Predicting the phase diagram of titanium dioxide with random search and pattern recognition
A Reinhardt, CJ Pickard, B Cheng
A Bone Morphogenetic Protein (BMP)-derived Peptide Based on the Type I Receptor-binding Site Modifies Cell-type Dependent BMP Signalling.
Z Tong, J Guo, RC Glen, NW Morrell, W Li
– Scientific Reports
(2019)
9,
13446
(DOI: 10.1038/s41598-019-49758-x)
Applying drug synergy metrics to oncology combination screening data: agreements, disagreements and pitfalls
AHC Vlot, N Aniceto, MP Menden, G Ulrich-Merzenich, A Bender
– Drug Discov Today
(2019)
(DOI: 10.1016/j.drudis.2019.09.002)
A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction
HGA Burton, AJW Thom
– Journal of Chemical Theory and Computation
(2019)
15,
4851
(DOI: 10.26434/chemrxiv.8089307)
Temperature Controls Guest Uptake and Release from Zn4L4 Tetrahedra.
D Zhang, TK Ronson, S Güryel, JD Thoburn, DJ Wales, JR Nitschke
– Journal of the American Chemical Society
(2019)
141,
14534
(DOI: 10.1021/jacs.9b07307)
Efficient formulation of full configuration interaction quantum Monte Carlo in a spin eigenbasis via the graphical unitary group approach.
W Dobrautz, SD Smart, A Alavi
– The Journal of Chemical Physics
(2019)
151,
094104
(DOI: 10.1063/1.5108908)
Accelerated relaxation and suppressed dynamic heterogeneity in a kinetically constrained (East) model with swaps
R Gutiérrez, JP Garrahan, RL Jack
– Journal of Statistical Mechanics Theory and Experiment
(2019)
2019,
094006
(DOI: 10.1088/1742-5468/ab39d8)
Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account.
G Drakakis, I Cortés-Ciriano, B Alexander-Dann, A Bender
– Curr Protoc Chem Biol
(2019)
11,
e73
(DOI: 10.1002/cpch.73)
A variational structure for interacting particle systems and their hydrodynamic scaling limits
M Kaiser, RL Jack, J Zimmer
– Communications in Mathematical Sciences
(2019)
17,
739
(DOI: 10.4310/cms.2019.v17.n3.a7)
The structural basis for membrane assembly of immunoreceptor signalling complexes.
N Dube, JK Marzinek, RC Glen, PJ Bond
– Journal of molecular modeling
(2019)
25,
277
(DOI: 10.1007/s00894-019-4165-6)
General Approach for Multireference Ground and Excited States Using Nonorthogonal Configuration Interaction
HGA Burton, AJW Thom
– Journal of Chemical Theory and Computation
(2019)
15,
4851
(DOI: 10.1021/acs.jctc.9b00441)
Finite field formalism for bulk electrolyte solutions
SJ Cox, M Sprik
– The Journal of Chemical Physics
(2019)
151,
064506
(DOI: 10.1063/1.5099207)
Similarity transformation of the electronic Schrödinger equation via Jastrow factorization
AJ Cohen, H Luo, K Guther, W Dobrautz, DP Tew, A Alavi
– The Journal of Chemical Physics
(2019)
151,
061101
(DOI: 10.1063/1.5116024)

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