• United Kingdom

Accepting PhD Students

PhD projects

Theoretical and computational chemistry Molecular Informatics

20032020

Research output per year

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Research Output

2020

Exploring ligand stability in protein crystal structures using binding pose metadynamics

Fusani, L., Palmer, D. S., Somers, D. O. & Wall, I. D., 23 Mar 2020, In : Journal of Chemical Information and Modeling . 60, 3, p. 1528-1539 12 p.

Research output: Contribution to journalArticle

Open Access
File
4 Downloads (Pure)

Multi-solvent models for solvation free energy predictions using 3D-RISM hydration thermodynamic descriptors

Subramanian, V., Ratkova, E., Palmer, D. S., Engkvist, O., Fedorov, M. V. & Llinas, A., 22 Jun 2020, In : Journal of Chemical Information and Modeling . 60, 6, p. 2977-2988 12 p.

Research output: Contribution to journalArticle

Rapid analysis of disease state in liquid human serum combining infrared spectroscopy and "digital drying"

Sala, A., Spalding, K. E., Ashton, K. M., Board, R., Butler, H. J., Dawson, T. P., Harris, D. A., Hughes, C. S., Jenkins, C. A., Jenkinson, M. D., Palmer, D. S., Smith, B. R., Thornton, C. A. & Baker, M. J., 1 Sep 2020, In : Journal of Biophotonics. 13, 9, 10 p., e202000118.

Research output: Contribution to journalArticle

Open Access
File
2 Downloads (Pure)

Stratifying brain tumour histological sub-types: the application of ATR-FTIR serum spectroscopy in secondary care

Cameron, J. M., Rinaldi, C., Butler, H. J., Hegarty, M. G., Brennan, P. M., Jenkinson, M. D., Syed, K., Ashton, K. M., Dawson, T. P., Palmer, D. S. & Baker, M. J., 27 Jun 2020, In : Cancers. 12, 7, 16 p., 1710.

Research output: Contribution to journalArticle

Open Access
File
2 Downloads (Pure)
2019

Developing infrared spectroscopic detection for stratifying brain tumour patients: glioblastoma multiforme vs. lymphoma

Cameron, J. M., Butler, H. J., Smith, B. R., Hegarty, M. G., Jenkinson, M. D., Syed, K., Brennan, P. M., Ashton, K., Dawson, T., Palmer, D. S. & Baker, M. J., 21 Nov 2019, In : Analyst. 144, 22, p. 6736-6750 15 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Development of high-throughput ATR-FTIR technology for rapid triage of brain cancer

Butler, H. J., Brennan, P. M., Cameron, J. M., Finlayson, D., Hegarty, M. G., Jenkinson, M. D., Palmer, D. S., Smith, B. R. & Baker, M. J., 8 Oct 2019, In : Nature Communications. 10, 9 p., 4501 .

Research output: Contribution to journalArticle

Open Access
File
11 Citations (Scopus)
7 Downloads (Pure)
2018

3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction

Sosnin, S., Misin, M., Palmer, D. S. & Fedorov, M. V., 19 Jul 2018, In : Journal of Physics: Condensed Matter. 30, 7 p., 32LT03 .

Research output: Contribution to journalArticle

Open Access
File
9 Citations (Scopus)
5 Downloads (Pure)

Biofluid spectroscopic disease diagnostics: a review on the processes and spectral impact of drying

Cameron, J. M., Butler, H. J., Palmer, D. S. & Baker, M. J., 30 Apr 2018, In : Journal of Biophotonics. 11, 4, 12 p., e201700299.

Research output: Contribution to journalReview article

Open Access
File
18 Citations (Scopus)
30 Downloads (Pure)

Comparative molecular field analysis using molecular integral equation theory

Ansari, S. M. & Palmer, D. S., 15 Mar 2018, In : Journal of Chemical Information and Modeling . 40 p.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
14 Downloads (Pure)

Health economic evaluation of a serum based blood test for brain tumour diagnosis: exploration of two clinical scenarios

Gray, E., Butler, H. J., Board, R., Brennan, P. M., Chalmers, A. J., Dawson, T., Goodden, J., Hamilton, W., Hegarty, M. G., James, A., Jenkinson, M. D., Kernick, D., Lekka, E., Livermore, L. J., Mills, S. J., O'Neill, K., Palmer, D. S., Vaqas, B. & Baker, M. J., 24 May 2018, In : BMJ Open. 8, 5, 9 p., e017593.

Research output: Contribution to journalArticle

Open Access
File
12 Citations (Scopus)
26 Downloads (Pure)

Optimal water networks in protein cavities with GAsol and 3D-RISM

Fusani, L., Wall, I., Palmer, D. & Cortes, A., 15 Jan 2018, In : Bioinformatics. 2 p.

Research output: Contribution to journalArticle

Open Access
File
5 Citations (Scopus)
7 Downloads (Pure)

Optimised spectral pre-processing for discrimination of biofluids via ATR-FTIR spectroscopy

Butler, H. J., Smith, B. R., Fritzsch, R., Radhakrishnan, P., Palmer, D. S. & Baker, M. J., 19 Nov 2018, In : Analyst.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)
8 Downloads (Pure)

PRFFECT: a versatile tool for spectroscopists

Smith, B. R., Baker, M. J. & Palmer, D. S., 15 Jan 2018, In : Chemometrics and Intelligent Laboratory Systems. 36 p.

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)
13 Downloads (Pure)
2017

On the effect of mutations in bovine or camel chymosin on the thermodynamics of binding κ-caseins

Ansari, S. M., Sørensen, J., Schiøtt, B. & Palmer, D. S., 30 Oct 2017, In : Proteins: Structure, Function, and Bioinformatics. p. 1-36 36 p.

Research output: Contribution to journalArticle

Open Access
File
11 Downloads (Pure)
2016

Allosteric activation mechanism of bovine chymosin revealed by bias-exchange metadynamics and molecular dynamics simulations

Ansari, S. M., Coletta, A., Kirkeby Skeby, K., Sørensen, J., Schiøtt, B. & Palmer, D. S., 14 Sep 2016, In : Journal of Physical Chemistry B. 120, 40, p. 10453-10462 10 p.

Research output: Contribution to journalArticle

Open Access
File
1 Citation (Scopus)
39 Downloads (Pure)

Are the sublimation thermodynamics of organic molecules predictable?

McDonagh, J., Palmer, D. S., van Mourik, T. & Mitchell, J. B. O., 17 Oct 2016, In : Journal of Chemical Information and Modeling . 52 p.

Research output: Contribution to journalArticle

Open Access
File
17 Citations (Scopus)
186 Downloads (Pure)

Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology

Smith, B. R., Ashton, K. M., Brodbelt, A., Dawson, T., Jenkinson, M. D., Hunt, N. T., Palmer, D. S. & Baker, M. J., 7 Jun 2016, In : Analyst. 141, p. 3668-3678 11 p.

Research output: Contribution to journalArticle

Open Access
File
24 Citations (Scopus)
112 Downloads (Pure)

Hydration free energies of molecular ions from theory and simulation

Misin, M., Fedorov, M. & Palmer, D., 11 Feb 2016, In : Journal of Physical Chemistry B. 120, 5, p. 975-983 9 p.

Research output: Contribution to journalArticle

Open Access
File
40 Citations (Scopus)
90 Downloads (Pure)

Molecular simulation methods to compute intrinsic aqueous solubility of crystalline drug-like molecules

Palmer, D. S. & Fedorov, M. V., 6 May 2016, Computational Pharmaceutical Solid State Chemistry. Abramov, Y. A. (ed.). Hoboken, NJ.: John Wiley & Sons Inc.

Research output: Chapter in Book/Report/Conference proceedingChapter

Predicting solvation free energies using parameter-free solvent models

Misin, M., Palmer, D. S. & Fedorov, M. V., 6 Jun 2016, In : Journal of Physical Chemistry B. 34 p.

Research output: Contribution to journalArticle

Open Access
File
12 Citations (Scopus)
62 Downloads (Pure)

Salting-out effects by pressure-corrected 3D-RISM

Misin, M., Vainikka, P. A., Fedorov, M. V. & Palmer, D. S., 20 Oct 2016, (Accepted/In press) In : Journal of Chemical Physics.

Research output: Contribution to journalArticle

Open Access
File
92 Downloads (Pure)
2015

Accurate hydration free energies at a wide range of temperatures from 3D-RISM

Misin, M., Fedorov, M. V. & Palmer, D. S., 7 Mar 2015, In : Journal of Chemical Physics. 142, 9, 6 p., 091105.

Research output: Contribution to journalArticle

Open Access
File
44 Citations (Scopus)
203 Downloads (Pure)

Fast and general method to predict the physicochemical properties of druglike molecules using the integral equation theory of molecular liquids

Palmer, D. S., Misin, M., Fedorov, M. V. & Llinas, A., 8 Sep 2015, In : Molecular Pharmaceutics. 12, 9, p. 3420–3432 13 p.

Research output: Contribution to journalArticle

Open Access
File
15 Citations (Scopus)
153 Downloads (Pure)

Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy

Ratkova, E. L., Palmer, D. S. & Fedorov, M. V., 2015, In : Chemical Reviews. 115, 13, p. 6312–6356 45 p.

Research output: Contribution to journalLiterature review

Open Access
File
104 Citations (Scopus)
198 Downloads (Pure)
2014

Is experimental data quality the limiting factor in predicting the aqueous solubility of druglike molecules?

Palmer, D. S. & Mitchell, J. B. O., 4 Aug 2014, In : Molecular Pharmaceutics. 11, 8, p. 2962–2972 11 p.

Research output: Contribution to journalArticle

Open Access
File
47 Citations (Scopus)
89 Downloads (Pure)

Is there a role for the integral equation theory of molecular liquids in chemical informatics?

Palmer, D. & Fedorov, M., 10 Aug 2014.

Research output: Contribution to conferenceSpeech

Solvation thermodynamics of biomolecules from the integral equation theory of molecular liquids

Palmer, D., Misin, M. & Fedorov, M., 20 Aug 2014, (Unpublished).

Research output: Contribution to conferenceSpeech

Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation

Somavarapu, A. K., Balakrishnan, S., Gautam, A. K. S., Palmer, D. & Venkatraman, P., 2014, In : BMC Structural Biology. 14, 9, 25 p.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)
204 Downloads (Pure)
2013

Computational biomolecular design: from drug discovery to bionanotechnology

Palmer, D., 27 Feb 2013.

Research output: Contribution to conferenceSpeech

Computing intrinsic aqueous solubility of crystalline organic molecules

Palmer, D., 12 Mar 2013, (Unpublished).

Research output: Contribution to conferencePoster

Computing intrinsic aqueous solubility of crystalline organic molecules

Palmer, D. & Fedorov, M., 4 Sep 2013.

Research output: Contribution to conferenceSpeech

Hot-spot mapping of the interactions between chymosin and bovine κ-casein

Sørensen, J., Palmer, D. & Schiøtt, B., 8 Jul 2013, In : Journal of Agricultural and Food Chemistry. 61, 33, p. 7949-7959 11 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Protein modelling using molecular integral equation theory: applications to chymosin—κ-casein complexes

Palmer, D., 15 Nov 2013, (Unpublished).

Research output: Contribution to conferencePoster

Solvent binding analysis and computational alanine scanning of the bovine chymosin-bovine κ-casein complex using molecular integral equation theory

Palmer, D., Sørensen, J. G. J. G., Schiøtt, B. B. & Fedorov, M. V. M. V., 10 Dec 2013, In : Journal of Chemical Theory and Computation . 9, 12, p. 5706-5717 12 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
2012

First principles calculation of the intrinsic aqueous solubility of crystalline druglike molecules

Palmer, D., McDonagh, J. L., Mitchell, J. B. O., van Mourik, T. & Fedorov, M., 11 Sep 2012, In : Journal of Chemical Theory and Computation . 8, 9, p. 3322–3337 16 p.

Research output: Contribution to journalArticle

51 Citations (Scopus)

In silico screening of bioactive solutes using molecular integral equation theory

Palmer, D., 27 Mar 2012.

Research output: Contribution to conferencePoster

File
50 Downloads (Pure)

In silico screening of bioactive solutes using molecular integral equation theory

Palmer, D., 14 Jun 2012.

Research output: Contribution to conferencePoster

File
104 Downloads (Pure)

Molecular Theories of Solvation: Applications to Biomolecular Thermodynamics

Palmer, D. & Fedorov, M., 26 Nov 2012, (Unpublished).

Research output: Contribution to conferencePoster

2011

Accurate calculation of the hydration free energies of biologically active molecules using the reference interaction site model

Palmer, D., Ratkova, E. L., Frolov, A. I., Sergiievskyi, V. P. & Fedorov, M. V., 27 Mar 2011, In : Abstracts of papers - American Chemical Society. 241, p. - 1 p.

Research output: Contribution to journalSpecial issue

Efficient predictions of physchem properties of biomolecules in aqueous solutions using the Reference Interaction Site Model

Fedorov, M. V., Frolov, A. I., Ratkova, E. L., Palmer, D. S. & Sergiievskyi, V. P., 28 Aug 2011, In : Abstracts of papers - American Chemical Society. 242

Research output: Contribution to journalArticle

Harmonic vibrational analysis in delocalized internal coordinates

Jensen, F. & Palmer, D. S., 2011, In : Journal of Chemical Theory and Computation . 7, 1, p. 223-230 8 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Hydration thermodynamics using the reference interaction site model: speed or accuracy?

Frolov, A. I., Ratkova, E. L., Palmer, D. & Fedorov, M. V., 19 May 2011, In : Journal of Physical Chemistry B. 115, 19, p. 6011-6022 12 p.

Research output: Contribution to journalArticle

49 Citations (Scopus)
19 Citations (Scopus)

In silico screening of bioactive and biomimetic solutes using Integral Equation Theory

Palmer, D. S., Chuev, G. N., Ratkova, E. L. & Fedorov, M. V., Jun 2011, In : Current Pharmaceutical Design. 17, 17, p. 1695-1708 14 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Predicting large-scale conformational changes in proteins using energy-weighted normal modes

Palmer, D. S. & Jensen, F., 1 Oct 2011, In : Proteins: Structure, Function, and Bioinformatics. 79, 10, p. 2778-2793 16 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Toward a universal model to calculate the solvation thermodynamics of druglike molecules: the importance of new experimental databases

Palmer, D., Frolov, A. I., Ratkova, E. L. & Fedorov, M. V., 2011, In : Molecular Pharmaceutics. 8, 4, p. 1423-1429 7 p.

Research output: Contribution to journalArticle

30 Citations (Scopus)
2010

Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model

Palmer, D., Sergiievskyi, V. P., Jensen, F. & Fedorov, M. V., 22 Jul 2010, In : Journal of Chemical Physics. 133, 4, 11 p., 044104.

Research output: Contribution to journalArticle

46 Citations (Scopus)