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David J. Huggins - Publications

Affiliations: 
Cavendish Laboratory University of Cambridge, Cambridge, England, United Kingdom 
Area:
Statistical Thermodynamics, Hydration, Computational Biology, Protein-protein Interactions, Drug Discovery
Website:
http://www.tcm.phy.cam.ac.uk/~djh210/
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Chen W, Cui D, Jerome SV, Michino M, Lenselink EB, Huggins DJ, Beautrait A, Vendome J, Abel R, Friesner RA, Wang L. Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations. Journal of Chemical Information and Modeling. PMID 37167486 DOI: 10.1021/acs.jcim.3c00013  0.354
2023 Sun S, Fushimi M, Rossetti T, Kaur N, Ferreira J, Miller M, Quast J, van den Heuvel J, Steegborn C, Levin LR, Buck J, Myers RW, Kargman S, Liverton N, Meinke PT, ... Huggins DJ, et al. Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. Journal of Chemical Information and Modeling. PMID 37060320 DOI: 10.1021/acs.jcim.2c01577  0.313
2022 Sun S, Huggins DJ. Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations. Frontiers in Molecular Biosciences. 9: 972162. PMID 36225254 DOI: 10.3389/fmolb.2022.972162  0.353
2022 Huggins DJ. Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation. 18: 2616-2630. PMID 35266690 DOI: 10.1021/acs.jctc.1c01208  0.375
2020 Huggins DJ. Structural analysis of experimental drugs binding to the SARS-CoV-2 target TMPRSS2. Journal of Molecular Graphics & Modelling. 100: 107710. PMID 32829149 DOI: 10.1016/J.Jmgm.2020.107710  0.355
2020 Wade AD, Huggins DJ. Identification of Optimal Ligand Growth Vectors Using an Alchemical Free-Energy Method. Journal of Chemical Information and Modeling. PMID 32810401 DOI: 10.1021/Acs.Jcim.0C00610  0.42
2020 Balbach M, Fushimi M, Huggins DJ, Steegborn C, Meinke PT, Levin LR, Buck J. Optimization of lead compounds into on-demand, non-hormonal contraceptives: leveraging a public-private drug discovery institute collaboration. Biology of Reproduction. PMID 32307523 DOI: 10.1093/Biolre/Ioaa052  0.313
2019 Sharma P, Mahen R, Rossmann M, Stokes JE, Hardwick B, Huggins DJ, Emery A, Kunciw DL, Hyvönen M, Spring DR, McKenzie GJ, Venkitaraman AR. A cryptic hydrophobic pocket in the polo-box domain of the polo-like kinase PLK1 regulates substrate recognition and mitotic chromosome segregation. Scientific Reports. 9: 15930. PMID 31685831 DOI: 10.1038/S41598-019-50702-2  0.33
2019 Wade AD, Huggins DJ. Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method. Journal of Chemical Theory and Computation. PMID 31584802 DOI: 10.1021/Acs.Jctc.9B00976  0.409
2019 Wade AD, Rizzi A, Wang Y, Huggins DJ. Computational Fluorine Scanning Using Free-Energy Perturbation. Journal of Chemical Information and Modeling. PMID 31046267 DOI: 10.1021/Acs.Jcim.9B00228  0.37
2019 Irwin BWJ, Vukovic S, Payne MC, Huggins DJ. A Large Scale Study of Hydration Environments Through Hydration Sites. The Journal of Physical Chemistry. B. PMID 31025866 DOI: 10.1021/Acs.Jpcb.9B02490  0.582
2018 Wade AD, Wang LP, Huggins DJ. Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties. Journal of Chemical Information and Modeling. PMID 30113842 DOI: 10.1021/Acs.Jcim.8B00166  0.368
2018 Irwin BWJ, Huggins DJ. Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation. Journal of Chemical Theory and Computation. PMID 29712434 DOI: 10.1021/Acs.Jctc.8B00027  0.405
2018 Vukovic S, Huggins DJ. Quantitative metrics for drug-target ligandability. Drug Discovery Today. PMID 29522887 DOI: 10.1016/J.Drudis.2018.02.015  0.319
2018 Huggins DJ, Biggin PC, Dämgen MA, Essex JW, Harris SA, Henchman RH, Khalid S, Kuzmanic A, Laughton CA, Michel J, Mulholland AJ, Rosta E, Sansom MSP, van der Kamp MW. Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity Wiley Interdisciplinary Reviews: Computational Molecular Science. 9: e1393. DOI: 10.1002/Wcms.1393  0.577
2017 Narvaez AJ, Ber S, Crooks A, Emery A, Hardwick B, Guarino Almeida E, Huggins DJ, Perera D, Roberts-Thomson M, Azzarelli R, Hood FE, Prior IA, Walker DW, Boyce R, Boyle RG, et al. Modulating Protein-Protein Interactions of the Mitotic Polo-like Kinases to Target Mutant KRAS. Cell Chemical Biology. PMID 28807782 DOI: 10.1016/J.Chembiol.2017.07.009  0.349
2017 Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL. Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction. Chemical Communications (Cambridge, England). PMID 28787041 DOI: 10.1039/C7Cc05379G  0.629
2017 Irwin BWJ, Huggins DJ. On the accuracy of one- and two-particle solvation entropies. The Journal of Chemical Physics. 146: 194111. PMID 28527450 DOI: 10.1063/1.4983654  0.343
2016 Huggins DJ. Studying the role of cooperative hydration in stabilizing folded protein states. Journal of Structural Biology. PMID 27633532 DOI: 10.1016/J.Jsb.2016.09.003  0.4
2016 Vukovic S, Brennan PE, Huggins DJ. Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 344007. PMID 27367338 DOI: 10.1088/0953-8984/28/34/344007  0.502
2016 Janeček M, Rossmann M, Sharma P, Emery A, Huggins DJ, Stockwell SR, Stokes JE, Tan YS, Almeida EG, Hardwick B, Narvaez AJ, Hyvönen M, Spring DR, McKenzie GJ, Venkitaraman AR. Allosteric modulation of AURKA kinase activity by a small-molecule inhibitor of its protein-protein interaction with TPX2. Scientific Reports. 6: 28528. PMID 27339427 DOI: 10.1038/Srep28528  0.399
2015 Laraia L, McKenzie G, Spring DR, Venkitaraman AR, Huggins DJ. Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions. Chemistry & Biology. 22: 689-703. PMID 26091166 DOI: 10.1016/J.Chembiol.2015.04.019  0.409
2015 Huggins DJ. Quantifying the entropy of binding for water molecules in protein cavities by computing correlations. Biophysical Journal. 108: 928-36. PMID 25692597 DOI: 10.1016/J.Bpj.2014.12.035  0.49
2015 Huggins DJ. Quantifying the entropy of binding for water molecules in protein cavities by computing correlations Biophysical Journal. 108: 928-936. DOI: 10.1016/j.bpj.2014.12.035  0.331
2014 Huggins DJ. Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm. Journal of Chemical Theory and Computation. 10: 3617-25. PMID 26588506 DOI: 10.1021/Ct500415G  0.361
2014 Huggins DJ. Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation Journal of Computational Chemistry. 35: 377-385. PMID 24311273 DOI: 10.1002/Jcc.23504  0.32
2013 Haider K, Huggins DJ. Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules Journal of Chemical Information and Modeling. 53: 2571-2586. PMID 24070451 DOI: 10.1021/Ci4003409  0.495
2013 Huggins DJ, Payne MC. Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes. The Journal of Physical Chemistry. B. 117: 8232-44. PMID 23763625 DOI: 10.1021/Jp4042233  0.558
2012 Huggins DJ. Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules Physical Chemistry Chemical Physics. 14: 15106-15117. PMID 23037989 DOI: 10.1039/C2Cp42631E  0.456
2012 Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. Journal of Medicinal Chemistry. 55: 6328-41. PMID 22708897 DOI: 10.1021/Jm300238H  0.532
2012 Huggins DJ. Benchmarking the thermodynamic analysis of water molecules around a model beta sheet Journal of Computational Chemistry. 33: 1383-1392. PMID 22457119 DOI: 10.1002/Jcc.22971  0.474
2012 Huggins DJ. Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models Journal of Chemical Physics. 136. PMID 22360206 DOI: 10.1063/1.3683447  0.39
2012 Huggins DJ, Sherman W, Tidor B. Rational approaches to improving selectivity in drug design Journal of Medicinal Chemistry. 55: 1424-1444. PMID 22239221 DOI: 10.1021/Jm2010332  0.509
2011 Huggins DJ, Marsh M, Payne MC. Thermodynamic Properties of Water Molecules at a Protein-Protein Interaction Surface. Journal of Chemical Theory and Computation. 7: 3514-3522. PMID 24554921 DOI: 10.1021/Ct200465Z  0.612
2011 Huggins DJ, Tidor B. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions Protein Engineering, Design and Selection. 24: 777-789. PMID 21771870 DOI: 10.1093/Protein/Gzr036  0.626
2011 Huggins DJ, Marsh M, Payne MC. Thermodynamic properties of water molecules at a protein-protein interaction surface Journal of Chemical Theory and Computation. 7: 3514-3522. DOI: 10.1021/ct200465z  0.526
2010 Huggins DJ, McKenzie GJ, Robinson DD, Narváez AJ, Hardwick B, Roberts-Thomson M, Venkitaraman AR, Grant GH, Payne MC. Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation Plos Computational Biology. 6. PMID 20711360 DOI: 10.1371/Journal.Pcbi.1000880  0.607
2009 Huggins DJ, Altman MD, Tidor B. Evaluation of an inverse molecular design algorithm in a model binding site Proteins: Structure, Function and Bioinformatics. 75: 168-186. PMID 18831031 DOI: 10.1002/Prot.22226  0.582
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