Quantum Mechanics/Molecular Mechanics Simulations Distinguish Insulin-Regulated Aminopeptidase Substrate (Oxytocin) and Inhibitor (Angiotensin IV) and Reveal Determinants of Activity and Inhibition.

David W. Wright 0001 Kuano, London, UK University College London, Centre for Computational Science, Department of Chemistry, UK https://davidwwright.netlify.app/ https://orcid.org/0000-0002-5124-8044 https://www.wikidata.org/entity/Q56957076 David W. Wright David W. Wright 0002 Emory University, School of Medicine, Atlanta, GA, USA David W. Wright 0003 Hewlett-Packard Labs David W. Wright 0004 Vanderbilt University, Department of Chemistry, Nashville, TN, USA

Marko Hanzevacki Rebecca M. Twidale Eric J. M. Lang Will Gerrard David W. Wright 0001 Vid Stojevic Adrian J. Mulholland Quantum Mechanics/Molecular Mechanics Simulations Distinguish Insulin-Regulated Aminopeptidase Substrate (Oxytocin) and Inhibitor (Angiotensin IV) and Reveal Determinants of Activity and Inhibition. 6261-6272 2025 65 J. Chem. Inf. Model. 12 https://doi.org/10.1021/acs.jcim.5c00869 https://www.wikidata.org/entity/Q135392153 db/journals/jcisd/jcisd65.html#HanzevackiTLGWSM25 streams/journals/jcisd

Shunzhou Wan Agastya P. Bhati David W. Wright 0001 Ian D. Wall Alan P. Graves Darren V. S. Green Peter V. Coveney Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. 2561-2570 2022 62 J. Chem. Inf. Model. 10 https://doi.org/10.1021/acs.jcim.2c00255 db/journals/jcisd/jcisd62.html#WanBWWGGC22

Derek Groen Robin A. Richardson David W. Wright 0001 Vytautas Jancauskas Robert Sinclair Paul Karlshoefer Maxime Vassaux Hamid Arabnejad Tomasz Piontek Piotr Kopta Bartosz Bosak Jalal Lakhlili Olivier Hoenen Diana Suleimenova Wouter Edeling Daan Crommelin Anna Nikishova Peter V. Coveney Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations. 479-492 2019 ICCS (4) https://doi.org/10.1007/978-3-030-22747-0_36 conf/iccS/2019-4 db/conf/iccS/iccS2019-4.html#GroenRWJSKVAPKB19

Jumana Dakka Matteo Turilli David W. Wright 0001 Stefan J. Zasada Vivek Balasubramanian Shunzhou Wan Peter V. Coveney Shantenu Jha High-throughput binding affinity calculations at extreme scales. 33-45 2018 19-S BMC Bioinform. 18 https://doi.org/10.1186/s12859-018-2506-6 https://www.wikidata.org/entity/Q60937560 db/journals/bmcbi/bmcbi19S.html#DakkaTWZBWCJ18

Jumana Dakka Kristof Farkas-Pall Vivek Balasubramanian Matteo Turilli Shunzhou Wan David W. Wright 0001 Stefan J. Zasada Peter V. Coveney Shantenu Jha Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive Algorithms to Reduce Time to Clinical Insight. 572-577 2018 CCGrid https://doi.org/10.1109/CCGRID.2018.00005 https://doi.ieeecomputersociety.org/10.1109/CCGRID.2018.00005 conf/ccgrid/2018 db/conf/ccgrid/ccgrid2018.html#DakkaFBTWWZCJ18 Jumana Dakka Kristof Farkas-Pall Matteo Turilli David W. Wright 0001 Peter V. Coveney Shantenu Jha Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations. 189-200 2018 eScience https://doi.org/10.1109/eScience.2018.00034 https://doi.ieeecomputersociety.org/10.1109/eScience.2018.00034 conf/eScience/2018 db/conf/eScience/eScience2018.html#DakkaFTWCJ18

Jumana Dakka Kristof Farkas-Pall Vivek Balasubramanian Matteo Turilli David W. Wright 0001 Shunzhou Wan Stefan J. Zasada Peter V. Coveney Shantenu Jha Rapid, concurrent and adaptive extreme scale binding free energy calculation. 2018 abs/1801.01174 CoRR http://arxiv.org/abs/1801.01174 db/journals/corr/corr1801.html#abs-1801-01174

David W. Wright 0001 Robin A. Richardson Peter V. Coveney Practical challenges for biomedical modeling using HPC. e27299 2018 6 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.27299v1 db/journals/peerjpre/peerjpre6.html#WrightRC18

Jumana Dakka Matteo Turilli David W. Wright 0001 Stefan J. Zasada Vivek Balasubramanian Shunzhou Wan Peter V. Coveney Shantenu Jha High-throughput Binding Affinity Calculations at Extreme Scales. 2017 abs/1712.09168 CoRR http://arxiv.org/abs/1712.09168 db/journals/corr/corr1712.html#abs-1712-09168

James M. Osborne Miguel O. Bernabeu Maria Bruna Ben Calderhead Jonathan Cooper Neil Dalchau Sara-Jane Dunn Alexander G. Fletcher Robin Freeman Derek Groen Bernhard Knapp Greg J. McInerny Gary R. Mirams Joe Pitt-Francis Biswa Sengupta David W. Wright 0001 Christian A. Yates David Gavaghan Stephen Emmott Charlotte M. Deane Ten Simple Rules for Effective Computational Research. 2014 10 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1003506 https://www.wikidata.org/entity/Q28974696 db/journals/ploscb/ploscb10.html#OsborneBBCCDDFFGKMMPSWYGED14

David W. Wright 0001 Peter V. Coveney Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations. 2636-2649 2011 51 J. Chem. Inf. Model. 10 https://doi.org/10.1021/ci200308r https://www.wikidata.org/entity/Q84915427 db/journals/jcisd/jcisd51.html#WrightC11

Owain Kenway David W. Wright 0001 Helmut Heller André Merzky Gavin J. Pringle Jules Wolfrat Peter V. Coveney Shantenu Jha Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences. 4:1-4:8 2011 TG https://doi.org/10.1145/2016741.2016746 conf/tg/2011 db/conf/tg/tg2011.html#Kenway0HMPWCJ11

S. Kashif Sadiq David W. Wright 0001 Owain Kenway Peter V. Coveney Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases. 890-905 2010 50 J. Chem. Inf. Model. 5 https://doi.org/10.1021/ci100007w https://www.wikidata.org/entity/Q43103118 db/journals/jcisd/jcisd50.html#SadiqWKC10

S. Kashif Sadiq David W. Wright 0001 Simon J. Watson 0002 Stefan J. Zasada Ileana Stoica Peter V. Coveney Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases. 1909-1919 2008 48 J. Chem. Inf. Model. 9 https://doi.org/10.1021/ci8000937 https://www.wikidata.org/entity/Q46424491 db/journals/jcisd/jcisd48.html#SadiqWWZSC08

Hamid Arabnejad Vivekanandan BalasubramanianVivek Balasubramanian Miguel O. Bernabeu Agastya BhatiAgastya P. Bhati Bartosz Bosak Maria Bruna Ben Calderhead Jonathan Cooper Peter V. Coveney Daan Crommelin Jumana Dakka Neil Dalchau Charlotte M. Deane Sara-Jane Dunn Wouter Edeling Stephen Emmott Kristof Farkas-Pall Alexander G. Fletcher Robin Freeman David Gavaghan Will Gerrard Alan P. Graves Darren V. S. Green Derek Groen Marko Hanzevacki Helmut Heller Olivier Hoenen Vytautas Jancauskas Shantenu Jha Paul Karlshoefer Owain Kenway Bernhard Knapp Piotr Kopta Jalal Lakhlili Eric J. M. Lang Greg J. McInerny André Merzky Gary R. Mirams Adrian J. Mulholland Anna Nikishova James M. Osborne Tomasz Piontek Joe Pitt-Francis Gavin J. Pringle Robin A. Richardson S. Kashif Sadiq Biswa Sengupta Robert Sinclair Ileana Stoica Vid Stojevic Diana Suleimenova Matteo Turilli Rebecca M. Twidale Maxime Vassaux Ian D. Wall Shunzhou Wan Simon J. Watson 0002 Jules Wolfrat Christian A. Yates Stefan J. Zasada