David Palmer

Research Output

Research Output per year

2003 2020

• 45 Article
• 6 Poster
• 5 Speech
• 1 Chapter
• 3 More
  • 1 Literature review
  • 1 Special issue
  • 1 Review article

Research Output per year

Research Output per year

Search results

• 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 journal › Article

  Open Access

  File

  • Ligands
  • Crystal structure
  • Proteins
  • Carrier concentration
  • Crystallography
  1 Citation (Scopus)

  10 Downloads (Pure)

• Interrogation of IDH1 status in gliomas by Fourier transform infrared spectroscopy

  Cameron, J. M., Conn, J. J. A., Rinaldi, C., Sala, A., Brennan, P. M., Jenkinson, M. D., Caldwell, H., Cinque, G., Syed, K., Butler, H. J., Hegarty, M. G., Palmer, D. S. & Baker, M. J., 8 Dec 2020, In : Cancers. 12, 12, 22 p., 3682.

  Research output: Contribution to journal › Article

  Open Access

  File
  1 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 journal › Article

  • Solvation
  • Free energy
  • Hydration
  • Thermodynamics
  • Organic solvents

• 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 journal › Article

  Open Access

  File

  • Infrared spectroscopy
  • Quantum cascade lasers
  • Drying
  • Infrared radiation
  • Liquids
  1 Citation (Scopus)

  4 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 journal › Article

  Open Access

  File

  • Spectroscopy
  • Tumors
  • Fourier transforms
  • Infrared radiation
  • Brain
  2 Citations (Scopus)

  6 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 journal › Article

  Open Access

  File

  • Tumors
  • Infrared radiation
  • Brain
  • Chemotherapy
  • Throughput
  6 Citations (Scopus)

  4 Downloads (Pure)

• 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 journal › Article

  Open Access

  File

  • Fourier transforms
  • Infrared radiation
  • Brain
  • Throughput
  • Fourier transform infrared spectroscopy
  16 Citations (Scopus)

  9 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 journal › Article

  Open Access

  File

  • Bioaccumulation
  • Spatial distribution
  • Neural networks
  • Molecules
  • Machine learning
  9 Citations (Scopus)

  7 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 journal › Article

  Open Access

  File

  • Integral equations
  • Atoms
  • Peptide Hydrolases
  • Molecular interactions
  • Ligands
  1 Citation (Scopus)

  18 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 journal › Article

  Open Access

  File

  • Tumors
  • Blood
  • Brain
  • Health
  • Economics
  13 Citations (Scopus)

  30 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 journal › Article

  Open Access

  File

  • Molecules
  • Proteins
  • Water
  • Protein Binding
  • Binding sites
  7 Citations (Scopus)

  10 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 journal › Article

  Open Access

  File

  • Spectroscopy
  • Infrared spectroscopy
  • Noise abatement
  • Brain
  • Derivatives
  10 Citations (Scopus)

  11 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 journal › Article

  Open Access

  File

  • Computer program listings
  • Testing
  9 Citations (Scopus)

  16 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 journal › Article

  Open Access

  File

  • Caseins
  • Thermodynamics
  • Milk
  • Proteolysis
  • Solvation
  13 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 journal › Article

  Open Access

  File

  • Casein
  • Caseins
  • Molecular dynamics
  • Chemical activation
  • Computer simulation
  1 Citation (Scopus)

  42 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 journal › Article

  Open Access

  File

  • Sublimation
  • Molecules
  • Thermodynamics
  • Free energy
  • Enthalpy
  17 Citations (Scopus)

  228 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 journal › Article

  Open Access

  File

  • Oncology
  • Biopsy
  • Brain
  • Machine learning
  • Fourier transforms
  25 Citations (Scopus)

  118 Downloads (Pure)

• Hydration free energies of molecular ions from theory and simulation

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

  Research output: Contribution to journal › Article

  Open Access

  File

  • Free energy
  • Hydration
  • Ions
  • Water
  41 Citations (Scopus)

  99 Downloads (Pure)

• 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 journal › Article

  Open Access

  File

  • Solvation
  • Free energy
  • Coulomb interactions
  • Olive oil
  • Olive Oil
  14 Citations (Scopus)

  75 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 journal › Article

  Open Access

  File

  • Organic compounds
  • Sodium chloride
  97 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 journal › Article

  Open Access

  File

  • Free energy
  • Hydration
  • Temperature
  • Molecular dynamics
  • Benchmarking
  46 Citations (Scopus)

  206 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 journal › Article

  Open Access

  File
  16 Citations (Scopus)

  165 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 journal › Article

  Open Access

  File
  54 Citations (Scopus)

  92 Downloads (Pure)

• 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 journal › Article

  Open Access

  File

  • Phosphorylation
  • Mass spectrometry
  • Conformations
  • Phosphotransferases
  • Proteins
  7 Citations (Scopus)

  209 Downloads (Pure)
• 2013

  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 journal › Article

  • Caseins
  • Enzymes
  • Mutagenesis
  • Cheeses
  • Substrates
  9 Citations (Scopus)

• 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 journal › Article

  • Casein
  • Caseins
  • Integral equations
  • Alanine
  • Milk
  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 journal › Article

  • Solubility
  • Crystalline materials
  • Molecules
  • Free energy
  • Crystal lattices
  56 Citations (Scopus)
• 2011

  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 journal › Article

  • Biomolecules

• 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 journal › Article

  • Principal component analysis
  • Set theory
  • Proteins
  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 journal › Article

  • Hydration
  • Thermodynamics
  • Free energy
  • Molecules
  49 Citations (Scopus)

• Initial stage of cheese production: a molecular modeling study of bovine and camel chymosin complexed with peptides from the chymosin-sensitive region of kappa-casein

  Sørensen, J., Palmer, D. S., Qvist, K. B. & Schiøtt, B., 1 May 2011, In : Journal of Agricultural and Food Chemistry. 59, 10, p. 5636-5647 12 p.

  Research output: Contribution to journal › Article

  • Molecular modeling
  • Cheeses
  • Caseins
  • Milk
  • Peptides
  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 journal › Article
  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 journal › Article

  • Proteins
  • Ligands
  • Molecular dynamics
  • Atoms
  • Principal component analysis
  6 Citations (Scopus)

• Predicting large-scale conformational changes in proteins using harmonic vibrational analyses

  Palmer, D. S. & Jensen, F., 27 Mar 2011, In : Abstracts of papers - American Chemical Society. 241

  Research output: Contribution to journal › Article

  • Proteins

• 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 journal › Article
  32 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 journal › Article

  • Free energy
  • Hydration
  • Molecules
  • Quantum theory
  • Systematic errors
  46 Citations (Scopus)

• Bovine chymosin: a computational study of recognition and binding of bovine kappa-casein

  Palmer, D. S., Christensen, A. U., Sørensen, J., Celik, L., Qvist, K. B. & Schiøtt, B., 1 Mar 2010, In : Biochemistry. 49, 11, p. 2563-2573 11 p.

  Research output: Contribution to journal › Article
  23 Citations (Scopus)

• Computational drug discovery: hydration behavior of de novo designed pharmaceuticals

  Palmer, D. & Fedorov, M., Nov 2010, In : G.I.T. Laboratory Journal Europe . p. 2-4 3 p.

  Research output: Contribution to journal › Article

  • Pharmacokinetics
  • Drug Discovery
  • Free energy
  • Drug products
  • Hydration

• Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction

  Palmer, D., Frolov, A. I., Ratkova, E. L. & Fedorov, M. V., 15 Dec 2010, In : Journal of Physics: Condensed Matter. 22, 49, p. - 9 p., 492101.

  Research output: Contribution to journal › Article

  • Density (specific gravity)
  • Free energy
  • Hydration
  • Molecules
  • Integral equations
  90 Citations (Scopus)
• 2008

  Predicting intrinsic aqueous solubility by a thermodynamic cycle

  Palmer, D. S., Llinas, A., Morao, I., Day, G. M., Goodman, J. M., Glen, R. C. & Mitchell, J. B., 2008, In : Molecular Pharmacology. 5, 2, p. 266-279 14 p.

  Research output: Contribution to journal › Article
  86 Citations (Scopus)

• Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction

  O'Boyle, N. M., Palmer, D. S., Nigsch, F. & Mitchell, J. BO., 2008, In : Chemistry Central Journal. 2, p. 21-21 1 p.

  Research output: Contribution to journal › Article

  Open Access

  File
  21 Citations (Scopus)

  22 Downloads (Pure)

• Why are some properties more difficult to predict than others? A study of QSPR models of solubility, melting point, and Log P

  Hughes, L. D., Palmer, D. S., Nigsch, F. & Mitchell, J. B., 1 Jan 2008, In : Journal of Chemical Information and Modeling . 48, 1, p. 220-232 13 p.

  Research output: Contribution to journal › Article
  127 Citations (Scopus)
• 2007

  Random forest models to predict aqueous solubility

  Palmer, D. S., O'Boyle, N. M., Glen, R. C. & Mitchell, J. B., 2007, In : Journal of Chemical Information and Modeling . 47, 1, p. 150-158 9 p.

  Research output: Contribution to journal › Article
  176 Citations (Scopus)
• 2006

  Chemoinformatics-based classification of prohibited substances employed for doping in sport

  Cannon, E. O., Bender, A., Palmer, D. S. & Mitchell, J. B., 2006, In : Journal of Chemical Information and Modeling . 46, 6, p. 2369-2380 12 p.

  Research output: Contribution to journal › Article
  28 Citations (Scopus)
• 2003

  Sequence-dependent DNA structure: a database of octamer structural parameters

  Gardiner, E. J., Hunter, C. A., Packer, M. J., Palmer, D. S. & Willett, P., 1 Oct 2003, In : Journal of Molecular Biology . 332, 5, p. 1025-1035 11 p.

  Research output: Contribution to journal › Article
  51 Citations (Scopus)