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Andrew D White - Publications

Affiliations: 
University of Rochester, Rochester, NY 
Area:
Chemistry, Chemical Engineering
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41 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 Wellawatte GP, Hocky GM, White AD. Neural potentials of proteins extrapolate beyond training data. The Journal of Chemical Physics. 159. PMID 37642255 DOI: 10.1063/5.0147240  0.749
2023 White AD, Hocky GM, Gandhi HA, Ansari M, Cox S, Wellawatte GP, Sasmal S, Yang Z, Liu K, Singh Y, Peña Ccoa WJ. Assessment of chemistry knowledge in large language models that generate code. Digital Discovery. 2: 368-376. PMID 37065678 DOI: 10.1039/d2dd00087c  0.726
2023 Wellawatte GP, Gandhi HA, Seshadri A, White AD. A Perspective on Explanations of Molecular Prediction Models. Journal of Chemical Theory and Computation. PMID 36972469 DOI: 10.1021/acs.jctc.2c01235  0.753
2022 Hocky GM, White AD. Natural language processing models that automate programming will transform chemistry research and teaching. Digital Discovery. 1: 79-83. PMID 35515080 DOI: 10.1039/d1dd00009h  0.743
2021 Li Z, Wellawatte GP, Chakraborty M, Gandhi HA, Xu C, White AD. Correction: Graph neural network based coarse-grained mapping prediction. Chemical Science. 12: 11922. PMID 34659733 DOI: 10.1039/d1sc90186a  0.747
2021 Yang Z, Chakraborty M, White AD. Predicting chemical shifts with graph neural networks. Chemical Science. 12: 10802-10809. PMID 34476061 DOI: 10.1039/d1sc01895g  0.59
2020 Li Z, Wellawatte GP, Chakraborty M, Gandhi HA, Xu C, White AD. Graph neural network based coarse-grained mapping prediction. Chemical Science. 11: 9524-9531. PMID 34123175 DOI: 10.1039/d0sc02458a  0.758
2020 Amirkulova DB, Chakraborty M, White AD. Experimentally Consistent Simulation of Aβ Peptide with a Minimal NMR Bias. The Journal of Physical Chemistry. B. PMID 32845146 DOI: 10.1021/Acs.Jpcb.0C07129  0.621
2020 Chakraborty M, Xu J, White AD. Is preservation of symmetry necessary for coarse-graining? Physical Chemistry Chemical Physics : Pccp. PMID 32596701 DOI: 10.1039/D0Cp02309D  0.614
2020 Barrett R, Chakraborty M, Amirkulova D, Gandhi H, Wellawatte G, White A. HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine Journal of Open Source Software. 5: 2367. DOI: 10.21105/joss.02367  0.738
2020 Chakraborty M, Ziatdinov M, Dyck O, Jesse S, White AD, Kalinin SV. Reconstruction of the interatomic forces from dynamic scanning transmission electron microscopy data Journal of Applied Physics. 127: 224301. DOI: 10.1063/5.0009413  0.576
2020 Li Z, Wellawatte GP, Chakraborty M, Gandhi HA, Xu C, White AD. Graph neural network based coarse-grained mapping prediction Chemical Science. 11: 9524-9531. DOI: 10.1039/D0Sc02458A  0.747
2020 Gandhi HA, Jakymiw S, Barrett R, Mahaseth H, White AD. Real-Time Interactive Simulation and Visualization of Organic Molecules Journal of Chemical Education. DOI: 10.1021/Acs.Jchemed.9B01161  0.758
2019 Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, ... ... White A, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8  0.759
2019 Amirkulova DB, White AD. Recent advances in maximum entropy biasing techniques for molecular dynamics Molecular Simulation. 45: 1285-1294. DOI: 10.1080/08927022.2019.1608988  0.316
2018 Chakraborty M, Xu C, White AD. Encoding and selecting coarse-grain mapping operators with hierarchical graphs. The Journal of Chemical Physics. 149: 134106. PMID 30292213 DOI: 10.1063/1.5040114  0.613
2018 Mayes HB, Lee S, White AD, Voth GA, Swanson JMJ. Multiscale kinetic modeling reveals ensemble of Cl-/H+ exchange pathways in ClC-ec1 antiporter. Journal of the American Chemical Society. PMID 29332400 DOI: 10.1021/Jacs.7B11463  0.449
2018 Amirkulova DB, White AD. Combining enhanced sampling with experiment-directed simulation of the GYG peptide Journal of Theoretical and Computational Chemistry. 17: 1840007. DOI: 10.1142/S0219633618400072  0.345
2018 Barrett R, Gandhi HA, Naganathan A, Daniels D, Zhang Y, Onwunaka C, Luehmann A, White AD. Social and Tactile Mixed Reality Increases Student Engagement in Undergraduate Lab Activities Journal of Chemical Education. 95: 1755-1762. DOI: 10.1021/Acs.Jchemed.8B00212  0.748
2018 Barrett R, Jiang S, White AD. Classifying antimicrobial and multifunctional peptides with Bayesian network models Peptide Science. 110: e24079. DOI: 10.1002/Pep2.24079  0.527
2017 White AD, Knight C, Hocky GM, Voth GA. Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data. The Journal of Chemical Physics. 146: 041102. PMID 28147531 DOI: 10.1063/1.4974837  0.756
2016 Dannenhoffer-Lafage T, White AD, Voth GA. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-grained Models. Journal of Chemical Theory and Computation. PMID 27045328 DOI: 10.1021/Acs.Jctc.6B00043  0.496
2015 White AD, Dama JF, Voth GA. Designing Free Energy Surfaces That Match Experimental Data with Metadynamics. Journal of Chemical Theory and Computation. 11: 2451-60. PMID 26575545 DOI: 10.1021/Acs.Jctc.5B00178  0.495
2015 White AD, Dama JF, Voth GA. Designing Free Energy Surfaces That Match Experimental Data with Metadynamics Journal of Chemical Theory and Computation. 11: 2451-2460. DOI: 10.1021/acs.jctc.5b00178  0.344
2014 White AD, Voth GA. Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data. Journal of Chemical Theory and Computation. 10: 3023-30. PMID 26588273 DOI: 10.1021/Ct500320C  0.492
2014 Nowinski AK, White AD, Keefe AJ, Jiang S. Biologically inspired stealth peptide-capped gold nanoparticles. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 1864-70. PMID 24483727 DOI: 10.1021/La404980G  0.753
2014 Shao Q, White AD, Jiang S. Difference of carboxybetaine and oligo(ethylene glycol) moieties in altering hydrophobic interactions: a molecular simulation study. The Journal of Physical Chemistry. B. 118: 189-94. PMID 24328129 DOI: 10.1021/Jp410224W  0.534
2014 Mi L, White AD, Shao Q, Setlow P, Li Y, Jiang S. Chemical insights into dodecylamine spore lethal germination Chemical Science. 5: 3320-3324. DOI: 10.1039/C4Sc01613K  0.748
2014 White AD, Voth GA. Efficient and minimal method to bias molecular simulations with experimental data Journal of Chemical Theory and Computation. 10: 3023-3030. DOI: 10.1021/ct500320c  0.388
2013 White AD, Keefe AJ, Ella-Menye JR, Nowinski AK, Shao Q, Pfaendtner J, Jiang S. Free energy of solvated salt bridges: a simulation and experimental study. The Journal of Physical Chemistry. B. 117: 7254-9. PMID 23697872 DOI: 10.1021/Jp4024469  0.76
2013 White AD, Keefe AJ, Nowinski AK, Shao Q, Caldwell K, Jiang S. Standardizing and simplifying analysis of peptide library data. Journal of Chemical Information and Modeling. 53: 493-9. PMID 23327110 DOI: 10.1021/Ci300484Q  0.756
2013 Brault ND, White AD, Taylor AD, Yu Q, Jiang S. Directly functionalizable surface platform for protein arrays in undiluted human blood plasma. Analytical Chemistry. 85: 1447-53. PMID 23298516 DOI: 10.1021/Ac303462U  0.472
2013 Keefe AJ, Caldwell KB, Nowinski AK, White AD, Thakkar A, Jiang S. Screening nonspecific interactions of peptides without background interference. Biomaterials. 34: 1871-7. PMID 23246063 DOI: 10.1016/J.Biomaterials.2012.11.014  0.757
2012 White AD, Huang W, Jiang S. Role of nonspecific interactions in molecular chaperones through model-based bioinformatics. Biophysical Journal. 103: 2484-91. PMID 23260050 DOI: 10.1016/J.Bpj.2012.10.040  0.514
2012 Shao Q, He Y, White AD, Jiang S. Different effects of zwitterion and ethylene glycol on proteins. The Journal of Chemical Physics. 136: 225101. PMID 22713073 DOI: 10.1063/1.4726135  0.492
2012 Nowinski AK, Sun F, White AD, Keefe AJ, Jiang S. Sequence, structure, and function of peptide self-assembled monolayers. Journal of the American Chemical Society. 134: 6000-5. PMID 22401132 DOI: 10.1021/Ja3006868  0.765
2012 White AD, Nowinski AK, Huang W, Keefe AJ, Sun F, Jiang S. Decoding nonspecific interactions from nature Chemical Science. 3: 3488. DOI: 10.1039/C2Sc21135A  0.761
2011 White A, Jiang S. Local and bulk hydration of zwitterionic glycine and its analogues through molecular simulations. The Journal of Physical Chemistry. B. 115: 660-7. PMID 21174438 DOI: 10.1021/Jp1067654  0.527
2011 White AD, Jiang S. Hydration of Zwitterionic Glycine Betaine and Analogues Through Molecular Simulation Biophysical Journal. 100: 212a. DOI: 10.1016/J.Bpj.2010.12.1372  0.528
2010 Shao Q, He Y, White AD, Jiang S. Difference in hydration between carboxybetaine and sulfobetaine. The Journal of Physical Chemistry. B. 114: 16625-31. PMID 21086974 DOI: 10.1021/Jp107272N  0.484
2009 Yang W, Zhang L, Wang S, White AD, Jiang S. Functionalizable and ultra stable nanoparticles coated with zwitterionic poly(carboxybetaine) in undiluted blood serum. Biomaterials. 30: 5617-21. PMID 19595457 DOI: 10.1016/J.Biomaterials.2009.06.036  0.463
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