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A Machine Learning Free Energy Functional for the 1D Reference Interaction Site Model: Towards Prediction of Solvation Free Energy for All Solvent Systems

Conn, J. G. M.; Ahmad, A.; Palmer, D. S.

Liquids, 2024, 4, 710-731

  • Open Access

  • Invited contribution to a Special Issue on "Recent Advances in the Behavior of Liquids" in Honor of Prof. Dr. William Acree Jr.

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bbSelect – An Open-Source Tool for Performing a 3D Pharmacophore-Driven Diverse Selection of R-groups
Rianjongdee, F.; Palmer, D. S.; Pickett, S.; Pogány, P.; Tomkinson, N.; Green, D. V. S.

J. Chem. Inf. Model. 2024, 64, 12, 4687–4699. DOI:10.1021/acs.jcim.4c00453

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Bioprocess Monitoring Applications of an Innovative ATR-FTIR Spectroscopy Platform

Christie, L.; Rutherford, S.; Palmer, D. S.; Baker, M. J.; Butler, H. J.

Front. Bioeng. Biotechnol. 2024, 12:1349473. DOI:10.3389/fbioe.2024.1349473

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Structure Guided Design of a Domain Selective Bromodomain and Extra Terminal (BET) N-Terminal Bromodomain Chemical Probe.

Bradley, E.; Fusani, L.; Chung, C.; Craggs, P.; Demont, E.; Humphreys, P.; Mitchell, D.; Phillipou, A.; Rioja, I.; Shah, R. R; Wellaway, C.; Prinjha, R.; Palmer, D. S.; Kerr, W.; Reid, M.; Wall, I.; Cookson, R.

J. Med. Chem., 2023, DOI:10.1021/acs.jmedchem.3c00906

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Rapid detection of heart failure using a spectroscopic liquid biopsy,

Christie, L.; Sala, A.; Cameron, J. M.; Conn, J. J. A.; Palmer, D. S.; McGeown, W. J.; Cannon, J. A.; McMurray, J. J. V; Quinn, T. J.; Sharp, J.; Baker, M. J.

Clinical Spectroscopy, 2023, DOI: 10.1016/j.clispe.2023.100029

  • Open Access

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A Spectroscopic Liquid Biopsy for the Earlier Detection of Multiple Cancer Types

Cameron, J. M.; Sala, A.; Antoniou G.; Brennan, P. M.; Butler, H. J.; Conn, J. J. A.; Connal, S.; Curran, T.; Hegarty, M. G.; McHardy, R. G.; Orringer, D.; Palmer, D. S.; Smith, B. R.; Baker, M. J. 

British Journal Of Cancer, 2023, 129, 1658–1666, DOI: 10.1038/s41416-023-02423-7

  • Open Access

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Global Serum Profiling: An Opportunity for Earlier Cancer Detection
Sala, A.; Cameron, J. M.; Brennan, P. M.; Crosbie, E. J.; Curran, T.; Gray, E.; Pierre, M-H. L.; Palmer, D. S.;  Rehman, I. U.; Rattray, N.; Baker, M. J.; J.

Exp. Clin. Cancer. Res., 2023, 42, 207. DOI: 10.1186/s13046-023-02786-y

  • Open Access

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Augmentation of FTIR Spectral Datasets Using Wasserstein Generative Adversarial Networks For Cancer Liquid Biopsies 

McHardy, R.G.; Antoniou, G.; Conn, J.J.A.; Baker, M. J.; Palmer, D. S.

Analyst, 2023, 148, 3860 - 3869. DOI: 10.1039/D3AN00669G

  • Open Access

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Recurrent Neural Networks for Time Domain Modelling of FTIR Spectra: Application to Brain Tumour Detection

Antoniou, G.; Conn, J. J. A.; Smith, B. R.; Brennan, P. M.; Baker, M. J.; Palmer, D. S.

Analyst, 2023, 148, 1770-1776. DOI: 10.1039/D2AN02041F

  • Open Access

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Solvation Entropy, Enthalpy and Free Energy Prediction using a Multi-task Deep Learning Functional in 1D-RISM

Fowles, D. J.; Palmer, D. S.

Phys. Chem. Chem. Phys.  2023, 25, 6944-6954. DOI: 10.1039/D3CP00199G

  • Open Access

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Liquid Biopsies: The Future of Cancer Early Detection

Connal, S.; Cameron, J. M; Sala, A.; Brennan, P. M.; Palmer, D. S.; Palmer, J. D.; Perlow, H.;  Baker, M. J. B.

J. Transl. Med. 2023, 21, 118.  DOI: 10.1186/s12967-023-03960-8

  • Open Access

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Blinded Predictions and Post-hoc Analysis of the Second Solubility Challenge Data: Exploring Training Data and Feature Set Selection for Machine and Deep Learning Models

Conn, J. G. M.;  Carter,J. W.; Conn, J. J. A.; Subramanian, V.;  Baxter, A.; Engkvist, O.; Llinas, A.; Ratkova, E. L;  Pickett, S. D.; McDonagh, J. L.; Palmer, D. S.

J. Chem. Inf. Model. 2023, 63, 1099–1113. DOI: 10.1021/acs.jcim.2c01189

  • Open Access

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Accurately Predicting Solvation Free Energy in Aqueous and Organic Solvents beyond 298K by Combining Deep Learning and the 1D Reference Interaction Site Model

Fowles, D.J.; McHardy, R. G.; Ahmad, A.; Palmer, D. S.

Digital Discovery, 2023, 2, 177-188. DOI: 10.1039/D2DD00103A

  • Open Access

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Pocket-size near-IR spectrometers for rapid examination of contaminated textile fibres at the crime-scene

Rashed, H. R.; Parrott, A. J..;  Nordon, A.; Baker, M. J.; Palmer, D. S.

Vibrational Spectroscopy, 2022, 123,103464. DOI: 10.1016/j.vibspec.2022.103464

  • Open Access

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Liquid Biopsy for Pancreatic Cancer Detection Using Infrared Spectroscopy

Sala, A.; Cameron, J. M.; Jenkins, C. A.; Barr, H.; Christie, L.; Conn, J. J. A.; Evans, T. R. J.; Harris, D. A.; Palmer, D. S.; Rinaldi, C.; Theakstone, A. G.; Baker, M. J.

Cancers, 2022, 14, 3048. DOI: 10.3390/cancers14133048

  • Open Access

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Clinical validation of a spectroscopic liquid biopsy for earlier detection of brain cancer

Cameron, J. M.; Brennan, P. M.; Antoniou G.; Butler, H. J.; Christie, L.; Conn, J. J. A.; Curran, T.; Gray, E.; Hegarty, M. G.; Jenkinson, M. D.; Orringer, D.; Palmer, D. S.; Sala, A.; Smith, B. R.; Baker, M. J.

Neuro-Oncol. Adv., 2022, 4, vdac024. DOI: 10.1093/noajnl/vdac024

  • Open Access

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​Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours

Theakstone, A. G.; Brennan, P. M.; Jenkinson, M. D.; Mills, S. J.; Syed, K.; Rinaldi, C.; Xu, Y.; Goodacre, R.; Butler, H. J.; Palmer, D. S.; Smith, B. R.; Baker, M. J.

Cancers, 2021, DOI: 10.3390/cancers13153851

  • Open Access

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Toward Physics-based Solubility Computation for Pharmaceuticals to Rival Informatics,

Fowles, D. J.; Palmer, D. S.; Guo, R.; Price, S. L.; Mitchell, J. B. O. 

J. Chem. Theory Comput. 2021, DOI: 10.1021/acs.jctc.1c00130

  • Open Access

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Early detection of brain tumours using a novel spectroscopic triage platform technology,

Brennan, P. M.; Butler, H. J.; Christie, L.; Hegarty, M. G.; Jenkinson, M. D.;  Keerie, C.; Norrie, J.;  Palmer, D. S.;  Smith, B. R.;  Baker, M. J.

Brain Communications, 2021, 3, fcab056 DOI: 10.1093/braincomms/fcab056

  • Open Access

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Early economic evaluation to guide the development of a spectroscopic liquid biopsy for the detection of brain cancer
Gray, E.; Cameron, J. M.; Butler, H. J.; Jenkinson, M. D.; Hegarty, M. G.; Palmer, D. S.; Brennan, P. M.; Baker, M. J.

Int. J. Technol. Assess. Health Care, 2021, 37, e4. DOI: 10.1017/S0266462321000143

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A Comparative Investigation of Two Handheld Near-IR Spectrometers for Direct Forensic Examination of Fibres In-situ.
Rashed, H. R.; Mishra, P.;  Nordon, A.; Palmer, D. S.; Baker, M. J.

Vibrational Spectroscopy, 2021, DOI: 10.1016/j.vibspec.2020.103205

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Exploring Ligand Stability in Protein Crystal Structures using Binding Pose Metadynamics

Fusani, L.;  Palmer, D. S.; Somers, D. O.; Wall, I. D.
J. Chem. Inf. Model. 2020, 60, 3. DOI: 10.1021/acs.jcim.9b00843

  • Open Access

 

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.

J. Chem. Inf. Model. 2020. DOI: 10.1021/acs.jcim.0c00065

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

Cameron, J. M.;  Rinaldi, C.; Butler, H. J.; Brennan, P. M.; Jenkinson, M. D.;  Syed, K.; Ashton, K.; Dawson, T.;  Palmer, D. S.; Baker, M. J. 

Cancers, 2020, 12, 1710; DOI: 10.3390/cancers12071710

  • Open Access

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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.

Cancers, 2020, 12, 3682; DOI: 10.3390/cancers12123682

  • Open Access

 

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.
J. Biophotonics, 2020, DOI: 10.1002/jbio.202000118

In-Silico Methods to Predict Solubility

McDonagh, J.; Mitchell J.B.O; Palmer, D.S.; Skyner R.

in “Solubility in Pharmaceutical Chemistry”, Saal, C. & Nair, A. (Ed's),  2019, pp 71–112. Berlin, Boston: De Gruyter. DOI: 10.1515/9783110559835-003

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

Butler, H. J.; Brennan, P. M.; Cameron, J.; Finlayson, D.; Hegarty, M.; Jenkinson, M. D.; Palmer, D. S.; Smith, B. R.; Baker, M, J.

Nature Communications, 2019, 10, 4501. DOI: 10.1038/s41467-019-12527-5

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Developing 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. A.; Dawson, T. P.; Palmer, D. S.; Baker, M. J.

Analyst, 2019, 144, 6736-6750. DOI: 10.1039/C9AN01731C

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

Sosnin, S; Misin, M; Palmer, D.; Fedorov, M.

J. Phys. Cond. Matt., 2018, 30, 32LT03

 

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

Fusani, L.; Wall, I.; Palmer, D. S.; Cortes, A.

Bioinformatics, 2018, 34, 1947–1948.  DOI: 10.1093/bioinformatics/bty024

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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.

Analyst, 2018, 143, 6121-6134. DOI: 10.1039/C8AN01384E

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Comparative Molecular Field Analysis using Molecular Integral Equation Theory.

Ansari, S.; Palmer D. S.

J. Chem. Inf. Model., 2018, 586, 1253-1265 DOI: 10.1021/acs.jcim.7b00600

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Early economic evaluation of a serum based blood test for brain tumours: Exploration of two clinical scenarios.

Gray,E.;  Butler, H. J.;  Board, R.; Brennan, P. M.;  Chalmers, A.;  Dawson, T.;  Goodden, J.; Hamilton, W.; Hegarty, M.G.;  James, A.; Jenkinson, M. D.;  Kernick, D.;  Lekka, E.;  Livermore, J.;  Mills, S. J.;  O’Neill, K.;  Vaqas, B.; Palmer, D. S.; Baker, M. J.; 

BMJ Open, 2018,8:e017593. DOI: 10.1136/bmjopen-2017-017593

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Biofluid Spectroscopic Disease Diagnostics: A Review on the Processes and Spectral Impact of Drying
Cameron, J. M.; Butler, H.; Palmer D. S.; Baker, M. J. ,

J. Biophotonics, 2018, 11:e201700299. DOI: 10.1002/jbio.201700299

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PRFFECT: A versatile tool for spectroscopists

Smith, B.; Baker, M.; Palmer D. S.

Chemom. Int. Lab. Sys. 2018, 172, 33-42/ DOI: 10.1016/j.chemolab.2017.10.024

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On The Effect of Mutations in Bovine or Camel Chymosin on the Thermodynamics of Binding κ-Caseins

Ansari, S.; Sørensen J.; Schiott, B.; Palmer, D. S.

Proteins, 2017, 86, 75–87.  DOI: 10.1002/prot.25410

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Salting-out Effects by Pressure-Corrected 3DRISM

Misin, M.; Vainikka, P.; Fedorov M. V.; Palmer D. S., 

J. Chem. Phys. 2016, 145, 19450. DOI: 10.1063/1.4966973

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Are the Sublimation Thermodynamics of Organic Molecules Predictable?  

McDonagh, J. L.; Palmer, D. S.; van Mourik, T.; Mitchell, J. B. O.  

J. Chem. Inf. Model., 2016, 56, 2162–2179, DOI: 10.1021/acs.jcim.6b00033

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Allosteric Activation Mechanism of Bovine Chymosin Revealed by Bias-Exchange Metadynamics and Molecular Dynamics Simulations

Ansari, S.; Coletta, A.; Kirkeby Skeby, K.; Sørensen J.; Schiott, B.; Palmer D.S.;

J. Phys. Chem. B., 2016, 120, 10453–10462. DOI: 10.1021/acs.jpcb.6b07491

 

Predicting Solvation Free Energies using Parameter-Free Solvent Models 

Misin, M.; Fedorov M. V.; Palmer D. S.

J. Phys. Chem. B, 2016, 120, 5724–5731. DOI: 10.1021/acs.jpcb.6b05352

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Predicting Intrinsic Aqueous Solubility from a Thermodynamic Cycle

Palmer, D. S.; Fedorov, M. V.

Chapter in  "Computational Approaches in Pharmaceutical Solid State Chemistry", Editor:  Yuriy A. Abramov, Wiley, 2016, ISBN: 9781118700747

 

Combining Random Forest and 2D Correlation Analysis to Identify Serum Spectral Signatures for Neurooncology

Smith, B. R.; Ashton, K.; Brodbelt, A.; Dawson, T.; Jenkinson, M.; Hunt, N.; Palmer, D.;  Baker, M. J. 

Analyst, 2016,  141, 3668-3678.  DOI: 10.1039/C5AN02452H

 

Hydration Free Energies of Molecular Ions from Theory and Simulation

Misin, M.; Fedorov M. V.; Palmer D. S.

J. Phys. Chem. B, 2016, 120, 975–983. DOI: 10.1021/acs.jpcb.5b10809

 

Fast and General Method to Predict the Physico-Chemical Properties of Druglike Molecules using the Integral Equation Theory of Molecular Liquids 

Palmer D. S.; Misin, M.; Fedorov, M. V.; Llinas, A.  

Mol. Pharmaceutics, 2015, 12, 3420−3432.  DOI: 10.1021/acs.molpharmaceut.5b00441

 

Solvation Thermodynamics of Organic Molecules by the Molecular Integral Equation Theory: Approaching Chemical Accuracy

Ratkova, E. L.; Palmer, D. S.; Fedorov, M. V.

Chem. Rev., 2015, 115, 6312–6356.  DOI: 10.1021/cr5000283

 

Accurate Hydration Free Energies at a wide range of temperatures from 3D RISM 

Misin, M.; Fedorov M. V.; Palmer D. S.

J. Chem. Phys., 2015, 142, 091105.  DOI: 10.1063/1.4914315

 

Is Experimental Data Quality the Limiting Factor in Predicting the Intrinsic Aqueous Solubility of Druglike Molecules?

Palmer D. S.; Mitchell J. B. O.

Mol. Pharmaceutics, 2014,  2014, 11, 2962−2972.  DOI: 10.1021/mp500103r

 

Structural Interrogation of Phosphoproteome Identified by Mass Spectrometry Reveals Allowed and Disallowed Regions of Phosphoconformation 

Somavarapu, A. K.; Balakrishnan, S.; Palmer, D. S.; Gautam, A. K. S. ; Venkatraman, P. 

BMC Structural Biology, 2014, 14,9. DOI: 10.1186/1472-6807-14-9

 

Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin — Bovine κ-Casein Complex using Molecular Integral Equation Theory

Palmer D. S.; Sorensen, J.; Schiøtt, B.; Fedorov, M. V.

J. Chem. Theory Comput., 2013, 9, 5706−5717. DOI: 10.1021/ct400605x

 

Hotspot Mapping the Interactions between Chymosin and Bovine kappa-casein

Sorensen, J.; Palmer D. S.;  Schiøtt, B.

J. Agr. Food Chem., 2013, 61, 7949-7959.  DOI: 10.1021/jf4021043

 

First Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

Palmer, D. S.; McDonagh, J. M.; Mitchell, J. B. O.; van Mourik, T; Fedorov, M. V.

J. Chem. Theory. Comput., 2012, 8, 3322-3337.  DOI: 10.1021/ct300345m

 

Predicting Large-Scale Conformational Changes in Proteins using Energy-Weighted Normal Modes

Palmer, D. S.; Jensen F. 

Proteins, 2011, 79,2778-2793.  DOI:10.1002/prot.23105

 

In silico screening of bioactive and biomimetic molecules using Molecular Integral Equation Theory

Palmer, D. S.; Chuev, G. N.; Ratkova, E. L.; Fedorov, M. V.

Curr. Pharm. Des., 2011, 17, 1695–1708. DOI: 10.2174/138161211796355065

 

Towards a Universal Model to Calculate the Hydration Free Energies of Druglike Molecules: The Importance of New Experimental Databases

Palmer, D. S.; Frolov, A. I.; Ratkova, E. L.; Fedorov, M. V.

Mol. Pharmaceutics, 2011, 8, 1423-1429. DOI: 10.1021/mp200119r

 

Hydration Thermodynamics using the Reference Interaction Site Model: Speed or Accuracy? 

Frolov, A. I.; Ratkova, E. L.; Palmer, D. S.; Fedorov, M. V. 

J Phys. Chem B. 2011, 115, 6011–6022.  DOI: 10.1021/jp111271c

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The Initial Stages of Cheese Manufacture - A Molecular Modelling Study of Bovine and Camel Chymosin-κ-Casein Complexes.

Sørensen, J.; Palmer, D. S.; Bruun Qvist, K; Schiøtt, B. H.

J. Agr. Food. Chem. 2011, 59, 5636–5647. DOI: 10.1021/jf104898w

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Computational Drug Discovery: Predicting the Hydration Behaviour of De Novo Designed Pharmaceuticals 

Palmer, D. S.; Fedorov M. V. 

G. I. T. Laboratory Journal, 2011. 1-2, 28-30

 

Harmonic Vibrational Analysis in Delocalised Internal Coordinates

Jensen, F. Palmer, D. S.

J. Chem. Theory Comput. 2011, 7, 223-230. DOI: 10.1021/ct100463a

 

Towards a Universal Method to Calculate Hydration Free Energies: 3D Reference Interaction Site Model with Partial Molar Volume Correction 

Palmer, D. S.; Frolov, A. I.; Ratkova, E. L.; Fedorov, M. V. 

J Phys. Cond. Matt. 2010, 22, 492101.  DOI:10.1088/0953-8984/22/49/492101

 

Accurate Calculation of the Hydration Free Energies of Druglike Molecules using the Reference Interaction Site Model 

Palmer, D. S.; Sergiievskyi, V. P.; Jensen, F.; Fedorov, M. V. 

J. Chem. Phys. 2010, 133, 044104.

 

Bovine Chymosin: A Computational Study of Binding and Recognition of Bovine κ-Casein

Palmer, D. S.; Christensen, A.; Sørensen, J.; Bruun Qvist, K.; Schiøtt, B. 

Biochemistry, 2010, 49, 2563-2573. DOI: 10.1021/bi902193u

 

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. B. O.

Chemistry Central Journal, 2008, 2:21. DOI: 10.1186/1752-153X-2-21

                       

Predicting Intrinsic Aqueous Solubility by a Thermodynamic Cycle 

Palmer, D. S.; Llinàs, A.; Morao, I;  Day, G. M.; Goodman, J. M.; Glen, R. C.; Mitchell, J. B. O.

Mol. Pharmaceutics.  2008, 5, 266-279.  DOI: 10.1021/mp7000878

  • The most accessed article in the journal from Jan­Mar, 2008.

  • One of the top 20 most-cited articles in the journal for the three years following its publication

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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. O. 

J. Chem. Inf. Model.  2008, 48, 220-232.  DOI: 10.1021/ci700307p

  • The fourth most accessed article in the journal from Jan­Mar, 2008

  • One of the top 20 most-cited articles in the journal for the three years following its publication

 

Random Forest Models to Predict Aqueous Solubility 

Palmer, D. S.; O'Boyle, N. M.; Glen, R. C.; Mitchell, J. B. O. 

J. Chem. Inf. Model. 2007, 47, 150-158.  DOI: 10.1021/ci060164k

  • The eleventh most accessed article in the journal from Jan­Mar, 2007.

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Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport

Cannon, E. O.; Bender, A.; Palmer, D. S.; Mitchell, J. B. O. 

J. Chem. Inf. Model. 2006, 46, 2369-2380.  DOI: 10.1021/ci0601160

 

Sequence-dependent DNA structure: A Database of Octamer Structural Parameters

Gardiner, E. J., Hunter, C. A., Packer, M. J., Palmer, D. S. & Willett, P.

J. Mol. Biol. 2003, 332, 1025-1035.  DOI: 10.1016/j.jmb.2003.08.006         

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