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Items: 1 to 50 of 212

1.

Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins.

Neelamraju S, Wales DJ, Gosavi S.

J Chem Inf Model. 2019 May 28;59(5):1703-1708. doi: 10.1021/acs.jcim.9b00007. Epub 2019 Apr 12.

PMID:
30977648
2.

Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling.

Chakraborty D, Wales DJ.

J Chem Phys. 2019 Mar 28;150(12):125101. doi: 10.1063/1.5070152.

PMID:
30927889
3.

Path Integral Energy Landscapes for Water Clusters.

Vaillant CL, Althorpe SC, Wales DJ.

J Chem Theory Comput. 2019 Jan 8;15(1):33-42. doi: 10.1021/acs.jctc.8b00675. Epub 2018 Dec 27.

PMID:
30550261
4.

Energy Landscape for Fold-Switching in Regulatory Protein RfaH.

Joseph JA, Chakraborty D, Wales DJ.

J Chem Theory Comput. 2019 Jan 8;15(1):731-742. doi: 10.1021/acs.jctc.8b00912. Epub 2018 Dec 26.

PMID:
30537824
5.

Computational Investigation of RNA A-Bulges Related to the Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism.

Wales DJ, Disney MD, Yildirim I.

J Phys Chem B. 2019 Jan 10;123(1):57-65. doi: 10.1021/acs.jpcb.8b09139. Epub 2019 Jan 2.

PMID:
30517788
6.

Energy Landscape of the Designed Protein Top7.

Neelamraju S, Gosavi S, Wales DJ.

J Phys Chem B. 2018 Dec 27;122(51):12282-12291. doi: 10.1021/acs.jpcb.8b08499. Epub 2018 Dec 12.

PMID:
30495947
7.

Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide.

Joseph JA, Wales DJ.

J Phys Chem B. 2018 Dec 20;122(50):11906-11921. doi: 10.1021/acs.jpcb.8b08371. Epub 2018 Dec 4.

PMID:
30433786
8.

Mapping Surface Hydrophobicity of α-Synuclein Oligomers at the Nanoscale.

Lee JE, Sang JC, Rodrigues M, Carr AR, Horrocks MH, De S, Bongiovanni MN, Flagmeier P, Dobson CM, Wales DJ, Lee SF, Klenerman D.

Nano Lett. 2018 Dec 12;18(12):7494-7501. doi: 10.1021/acs.nanolett.8b02916. Epub 2018 Nov 7.

9.

Mutational Basin-Hopping: Combined Structure and Sequence Optimization for Biomolecules.

Röder K, Wales DJ.

J Phys Chem Lett. 2018 Nov 1;9(21):6169-6173. doi: 10.1021/acs.jpclett.8b02839. Epub 2018 Oct 11.

PMID:
30299103
10.

Analysis of the Ub to Ub-CR Transition in Ubiquitin.

Röder K, Wales DJ.

Biochemistry. 2018 Oct 30;57(43):6180-6186. doi: 10.1021/acs.biochem.8b00770. Epub 2018 Oct 15.

PMID:
30265521
11.

Effects of random pinning on the potential energy landscape of a supercooled liquid.

Niblett SP, de Souza VK, Jack RL, Wales DJ.

J Chem Phys. 2018 Sep 21;149(11):114503. doi: 10.1063/1.5042140.

PMID:
30243283
12.

Proline provides site-specific flexibility for in vivo collagen.

Chow WY, Forman CJ, Bihan D, Puszkarska AM, Rajan R, Reid DG, Slatter DA, Colwell LJ, Wales DJ, Farndale RW, Duer MJ.

Sci Rep. 2018 Sep 14;8(1):13809. doi: 10.1038/s41598-018-31937-x.

13.

Terahertz VRT Spectroscopy of the Water Hexamer-h12 Cage: Dramatic Libration-Induced Enhancement of Hydrogen Bond Tunneling Dynamics.

Cole WTS, Yönder Ö, Sheikh AA, Fellers RS, Viant MR, Saykally RJ, Farrell JD, Wales DJ.

J Phys Chem A. 2018 Sep 20;122(37):7421-7426. doi: 10.1021/acs.jpca.8b05777. Epub 2018 Sep 10.

PMID:
30148958
14.

Computational Studies of the Mechanical Stability for Single-Strand Break DNA.

Krupa P, Wales DJ, Sieradzan AK.

J Phys Chem B. 2018 Aug 30;122(34):8166-8173. doi: 10.1021/acs.jpcb.8b05417. Epub 2018 Aug 16.

PMID:
30080414
15.

Predicting Pathways between Distant Configurations for Biomolecules.

Röder K, Wales DJ.

J Chem Theory Comput. 2018 Aug 14;14(8):4271-4278. doi: 10.1021/acs.jctc.8b00370. Epub 2018 Jul 17.

16.

Tunneling splittings from path-integral molecular dynamics using a Langevin thermostat.

Vaillant CL, Wales DJ, Althorpe SC.

J Chem Phys. 2018 Jun 21;148(23):234102. doi: 10.1063/1.5029258.

PMID:
29935506
17.

Loss surface of XOR artificial neural networks.

Mehta D, Zhao X, Bernal EA, Wales DJ.

Phys Rev E. 2018 May;97(5-1):052307. doi: 10.1103/PhysRevE.97.052307.

PMID:
29906831
18.

Evolved Minimal Frustration in Multifunctional Biomolecules.

Röder K, Wales DJ.

J Phys Chem B. 2018 Dec 13;122(49):10989-10995. doi: 10.1021/acs.jpcb.8b03632. Epub 2018 Jun 11.

PMID:
29799199
19.

Energy Landscapes of Mini-Dumbbell DNA Octanucleotides.

Klimavicz JS, Röder K, Wales DJ.

J Chem Theory Comput. 2018 Jul 10;14(7):3870-3876. doi: 10.1021/acs.jctc.8b00262. Epub 2018 Jun 8.

20.

From sticky-hard-sphere to Lennard-Jones-type clusters.

Trombach L, Hoy RS, Wales DJ, Schwerdtfeger P.

Phys Rev E. 2018 Apr;97(4-1):043309. doi: 10.1103/PhysRevE.97.043309.

PMID:
29758765
21.

3D-Printable Photochromic Molecular Materials for Reversible Information Storage.

Wales DJ, Cao Q, Kastner K, Karjalainen E, Newton GN, Sans V.

Adv Mater. 2018 Jun;30(26):e1800159. doi: 10.1002/adma.201800159. Epub 2018 Apr 30.

PMID:
29707849
22.

Exploring Energy Landscapes.

Wales DJ.

Annu Rev Phys Chem. 2018 Apr 20;69:401-425. doi: 10.1146/annurev-physchem-050317-021219.

PMID:
29677468
23.

Shining a light on the photo-sensitisation of organic-inorganic hybrid polyoxometalates.

Cameron JM, Wales DJ, Newton GN.

Dalton Trans. 2018 Apr 17;47(15):5120-5136. doi: 10.1039/c8dt00400e.

PMID:
29517788
24.

Energy Landscapes for the Aggregation of Aβ17-42.

Röder K, Wales DJ.

J Am Chem Soc. 2018 Mar 21;140(11):4018-4027. doi: 10.1021/jacs.7b12896. Epub 2018 Mar 8.

25.

Structure, thermodynamics, and rearrangement mechanisms in gold clusters-insights from the energy landscapes framework.

Schebarchov D, Baletto F, Wales DJ.

Nanoscale. 2018 Jan 25;10(4):2004-2016. doi: 10.1039/c7nr07123j.

26.

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

Chakraborty D, Wales DJ.

J Phys Chem Lett. 2018 Jan 4;9(1):229-241. doi: 10.1021/acs.jpclett.7b01933. Epub 2017 Dec 28.

PMID:
29240425
27.

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.

Cragnolini T, Chakraborty D, Šponer J, Derreumaux P, Pasquali S, Wales DJ.

J Chem Phys. 2017 Oct 21;147(15):152715. doi: 10.1063/1.4997377.

PMID:
29055346
28.

Pathways for diffusion in the potential energy landscape of the network glass former SiO2.

Niblett SP, Biedermann M, Wales DJ, de Souza VK.

J Chem Phys. 2017 Oct 21;147(15):152726. doi: 10.1063/1.5005924.

PMID:
29055343
29.

Structure and Thermodynamics of Metal Clusters on Atomically Smooth Substrates.

Eckhoff M, Schebarchov D, Wales DJ.

J Phys Chem Lett. 2017 Nov 2;8(21):5402-5407. doi: 10.1021/acs.jpclett.7b02543. Epub 2017 Oct 23.

PMID:
29043810
30.

Prediction of early unplanned intensive care unit readmission in a UK tertiary care hospital: a cross-sectional machine learning approach.

Desautels T, Das R, Calvert J, Trivedi M, Summers C, Wales DJ, Ercole A.

BMJ Open. 2017 Sep 15;7(9):e017199. doi: 10.1136/bmjopen-2017-017199.

31.

Properties of kinetic transition networks for atomic clusters and glassy solids.

Morgan JWR, Mehta D, Wales DJ.

Phys Chem Chem Phys. 2017 Sep 27;19(37):25498-25508. doi: 10.1039/c7cp03346j.

PMID:
28900644
32.

Optimal Alignment of Structures for Finite and Periodic Systems.

Griffiths M, Niblett SP, Wales DJ.

J Chem Theory Comput. 2017 Oct 10;13(10):4914-4931. doi: 10.1021/acs.jctc.7b00543. Epub 2017 Sep 14.

PMID:
28841314
33.

Machine learning landscapes and predictions for patient outcomes.

Das R, Wales DJ.

R Soc Open Sci. 2017 Jul 26;4(7):170175. doi: 10.1098/rsos.170175. eCollection 2017 Jul.

34.

Decoupled Associative and Dissociative Processes in Strong yet Highly Dynamic Host-Guest Complexes.

Appel EA, Biedermann F, Hoogland D, Del Barrio J, Driscoll MD, Hay S, Wales DJ, Scherman OA.

J Am Chem Soc. 2017 Sep 20;139(37):12985-12993. doi: 10.1021/jacs.7b04821. Epub 2017 Sep 8.

PMID:
28661667
35.

Energy landscapes and dynamics of glycine on Cu(110).

Sacchi M, Wales DJ, Jenkins SJ.

Phys Chem Chem Phys. 2017 Jun 28;19(25):16600-16605. doi: 10.1039/c7cp02716h.

PMID:
28657633
36.

Exploring biomolecular energy landscapes.

Joseph JA, Röder K, Chakraborty D, Mantell RG, Wales DJ.

Chem Commun (Camb). 2017 Jun 27;53(52):6974-6988. doi: 10.1039/c7cc02413d. Review.

PMID:
28489083
37.

Decoding heat capacity features from the energy landscape.

Wales DJ.

Phys Rev E. 2017 Mar;95(3-1):030105. doi: 10.1103/PhysRevE.95.030105. Epub 2017 Mar 22.

PMID:
28415307
38.

Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems.

de Souza VK, Stevenson JD, Niblett SP, Farrell JD, Wales DJ.

J Chem Phys. 2017 Mar 28;146(12):124103. doi: 10.1063/1.4977794.

PMID:
28388104
39.

Energy landscapes for machine learning.

Ballard AJ, Das R, Martiniani S, Mehta D, Sagun L, Stevenson JD, Wales DJ.

Phys Chem Chem Phys. 2017 May 24;19(20):12585-12603. doi: 10.1039/c7cp01108c.

PMID:
28367548
40.

Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field.

Wales DJ, Yildirim I.

J Phys Chem B. 2017 Apr 13;121(14):2989-2999. doi: 10.1021/acs.jpcb.7b00819. Epub 2017 Mar 31.

PMID:
28319659
41.

What Makes Telomeres Unique?

Sieradzan AK, Krupa P, Wales DJ.

J Phys Chem B. 2017 Mar 16;121(10):2207-2219. doi: 10.1021/acs.jpcb.6b08780. Epub 2017 Mar 1.

PMID:
28194966
42.

Atomic clusters with addressable complexity.

Wales DJ.

J Chem Phys. 2017 Feb 7;146(5):054306. doi: 10.1063/1.4974838.

PMID:
28178805
43.

Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations.

Röder K, Wales DJ.

J Chem Theory Comput. 2017 Mar 14;13(3):1468-1477. doi: 10.1021/acs.jctc.7b00024. Epub 2017 Feb 8.

44.

Dynamics and thermodynamics of the coronene octamer described by coarse-grained potentials.

Hernández-Rojas J, Calvo F, Niblett S, Wales DJ.

Phys Chem Chem Phys. 2017 Jan 18;19(3):1884-1895. doi: 10.1039/c6cp07671h.

PMID:
28009856
45.

Surface-based molecular self-assembly: Langmuir-Blodgett films of amphiphilic Ln(III) complexes.

Wales DJ, Kitchen JA.

Chem Cent J. 2016 Nov 28;10:72. eCollection 2016. Review.

46.

GPU-Accelerated Exploration of Biomolecular Energy Landscapes.

Mantell RG, Pitt CE, Wales DJ.

J Chem Theory Comput. 2016 Dec 13;12(12):6182-6191. Epub 2016 Nov 22.

47.

Probing helical transitions in a DNA duplex.

Chakraborty D, Wales DJ.

Phys Chem Chem Phys. 2016 Dec 21;19(1):878-892. doi: 10.1039/c6cp06309h.

PMID:
27942647
48.

Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification.

Joseph JA, Whittleston CS, Wales DJ.

J Chem Theory Comput. 2016 Dec 13;12(12):6109-6117. Epub 2016 Nov 15.

PMID:
27809512
49.

Impurity effects on solid-solid transitions in atomic clusters.

Husic BE, Schebarchov D, Wales DJ.

Nanoscale. 2016 Nov 3;8(43):18326-18340.

PMID:
27775141
50.

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J.

J Chem Theory Comput. 2016 Dec 13;12(12):6077-6097. Epub 2016 Nov 11.

PMID:
27767303

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