skip to content
 

Recent Publications from the Theory Research Interest Group

Exploring biomolecular energy landscapes.
JA Joseph, K Röder, D Chakraborty, RG Mantell, DJ Wales
– Chemical communications (Cambridge, England)
(2017)
Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure.
DJ Mason, I Stott, S Ashenden, ZB Weinstein, I Karakoc, S Meral, N Kuru, A Bender, M Cokol
– J Med Chem
(2017)
60,
3902
Projector Quantum Monte Carlo Method for Nonlinear Wave Functions
LR Schwarz, A Alavi, GH Booth
– Phys Rev Lett
(2017)
118,
176403
Polypharmacological In Silico Bioactivity Profiling and Experimental Validation Uncovers Sedative-Hypnotic Effects of Approved and Experimental Drugs in Rat
G Drakakis, KA Wafford, SC Brewerton, MJ Bodkin, DA Evans, A Bender
– ACS Chem Biol
(2017)
Emergence of complex behavior in pili-based motility in early stages of P. aeruginosa surface adaptation
Y Brill-Karniely, F Jin, GCL Wong, D Frenkel, J Dobnikar
– Scientific reports
(2017)
7,
45467
Energy landscapes for machine learning
AJ Ballard, R Das, S Martiniani, D Mehta, L Sagun, JD Stevenson, DJ Wales
– Physical chemistry chemical physics : PCCP
(2017)
Nanoparticle assembly: A perspective and some unanswered questions
SK Kumar, G Kumaraswamy, BLV Prasad, R Bandyopadhyaya, S Granick, O Gang, VN Manoharan, D Frenkel, NA Kotov
– Current Science
(2017)
112,
1635
Identification of Novel Class of Triazolo-Thiadiazoles as Potent Inhibitors of Human Heparanase and their Anticancer Activity.
CP Baburajeev, CD Mohan, S Rangappa, DJ Mason, JE Fuchs, A Bender, U Barash, I Vlodavsky, Basappa, KS Rangappa
– BMC cancer
(2017)
17,
235
Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised alpha/gamma Torsional Parameters for the Amber Force Field
DJ Wales, I Yildirim
– J Phys Chem B
(2017)
121,
2989
Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems
VK de Souza, JD Stevenson, SP Niblett, JD Farrell, DJ Wales
– The Journal of chemical physics
(2017)
146,
124103
Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson’s disease: a comparison of 33 human and animal studies
E Oerton, A Bender
– BMC Neurology
(2017)
17,
58
Semistochastic Heat-Bath Configuration Interaction Method: Selected Configuration Interaction with Semistochastic Perturbation Theory
S Sharma, AA Holmes, G Jeanmairet, A Alavi, CJ Umrigar
– Journal of Chemical Theory and Computation
(2017)
13,
1595
Decoding heat capacity features from the energy landscape.
DJ Wales
– Phys Rev E
(2017)
95,
030105
Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations.
K Röder, DJ Wales
– Journal of Chemical Theory and Computation
(2017)
13,
1468
Toward Understanding the Cold, Hot, and Neutral Nature of Chinese Medicines Using in Silico Mode-of-Action Analysis.
X Fu, LH Mervin, X Li, H Yu, J Li, SZ Mohamad Zobir, A Zoufir, Y Zhou, Y Song, Z Wang, A Bender
– J Chem Inf Model
(2017)
57,
468
Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations
K Roder, DJ Wales
– JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2017)
13,
1468
What Makes Telomeres Unique?
AK Sieradzan, P Krupa, DJ Wales
– J Phys Chem B
(2017)
121,
2207
Phase Transitions in Biological Systems with Many Components
WM Jacobs, D Frenkel
– Biophys J
(2017)
112,
683
Investigating the role of boundary bricks in DNA brick self-assembly.
HK Wayment-Steele, D Frenkel, A Reinhardt
– Soft Matter
(2017)
13,
1670
Improving Screening Efficiency through Iterative Screening Using Docking and Conformal Prediction
F Svensson, U Norinder, A Bender
– J Chem Inf Model
(2017)
57,
439