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Jianing Li, Ph.D. - Publications

Affiliations: 
2011 Chemistry Columbia University, New York, NY 
Area:
Computational Chemistry
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48 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 Thapa S, Clark F, Schneebeli ST, Li J. Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study. Journal of Chemical Theory and Computation. PMID 38013425 DOI: 10.1021/acs.jctc.3c00699  0.609
2023 McCarthy DR, Remington JM, Ferrell JB, Schneebeli ST, Li J. Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin. Journal of Chemical Theory and Computation. PMID 37877553 DOI: 10.1021/acs.jctc.3c00720  0.586
2023 Corteselli EM, Sharafi M, Hondal R, MacPherson M, White S, Lam YW, Gold C, Manuel AM, van der Vliet A, Schneebeli ST, Anathy V, Li J, Janssen-Heininger YMW. Structural and functional fine mapping of cysteines in mammalian glutaredoxin reveal their differential oxidation susceptibility. Nature Communications. 14: 4550. PMID 37507364 DOI: 10.1038/s41467-023-39664-2  0.609
2023 Remington JM, McKay KT, Beckage NB, Ferrell JB, Schneebeli ST, Li J. GPCRLigNet: rapid screening for GPCR active ligands using machine learning. Journal of Computer-Aided Molecular Design. 37: 147-156. PMID 36840893 DOI: 10.1007/s10822-023-00497-2  0.601
2022 Murphy KE, McKay KT, Schenkelberg M, Sharafi M, Vestrheim O, Ivancic M, Li J, Schneebeli ST. Helical Molecular Springs with Varying Spring Constants. Angewandte Chemie (International Ed. in English). PMID 36161747 DOI: 10.1002/anie.202209772  0.619
2022 McKay K, Hamilton NB, Remington JM, Schneebeli ST, Li J. Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery. Frontiers in Molecular Biosciences. 9: 879212. PMID 35847975 DOI: 10.3389/fmolb.2022.879212  0.63
2022 Li J, Remington JM, Liao C, Parsons RL, Schneebeli S, Braas KM, May V, Brewer M. GPCR Intracellular Loop Regulation of Beta-Arrestin-Mediated Endosomal Signaling Dynamics. Journal of Molecular Neuroscience : Mn. PMID 35538393 DOI: 10.1007/s12031-022-02016-8  0.592
2022 Remington JM, Ferrell JB, Schneebeli ST, Li J. Concerted Rolling and Penetration of Peptides during Membrane Binding. Journal of Chemical Theory and Computation. PMID 35507824 DOI: 10.1021/acs.jctc.2c00014  0.593
2021 Rajappan SC, Vestrheim O, Sharafi M, Li J, Schneebeli ST. Carbonyl-to-Alkyne Electron Donation Effects in up to 10-nm-Long, Unimolecular Oligo(-phenylene ethynylenes). Organic Materials. 3: 337-345. PMID 34505058 DOI: 10.1055/s-0041-1730899  0.596
2021 Zhao X, Remington JM, Schneebeli ST, Arold ST, Li J. Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament. The Journal of Physical Chemistry Letters. 7878-7884. PMID 34382809 DOI: 10.1021/acs.jpclett.1c01710  0.59
2021 Li J, McKay KT, Remington JM, Schneebeli ST. A computational study of cooperative binding to multiple SARS-CoV-2 proteins. Scientific Reports. 11: 16307. PMID 34381116 DOI: 10.1038/s41598-021-95826-6  0.602
2021 Remington JM, McKay KT, Ferrell JB, Schneebeli ST, Li J. Enhanced Sampling Protocol to Elucidate Fusion Peptide Opening of SARS-CoV-2 Spike Protein. Biophysical Journal. PMID 34087207 DOI: 10.1016/j.bpj.2021.05.022  0.628
2021 Jaynes TJ, Sharafi M, Campbell JP, Bocanegra J, McKay KT, Little K, Osadchey Brown R, Gray DL, Woods TJ, Li J, Schneebeli ST. Iterative Exponential Growth of Oxygen-Linked Aromatic Polymers Driven by Nucleophilic Aromatic Substitution Reactions. Frontiers in Chemistry. 9: 620017. PMID 33996739 DOI: 10.3389/fchem.2021.620017  0.598
2020 Remington JM, Ferrell JB, Zorman M, Petrucci A, Schneebeli ST, Li J. Machine Learning in a Molecular Modeling Course for Chemistry, Biochemistry, and Biophysics Students. Biophysicist (Rockville, Md.). 1. PMID 34337350 DOI: 10.35459/tbp.2019.000140  0.556
2020 Remington JM, Liao C, Sharafi M, Ste Marie EJ, Ferrell JB, Hondal RJ, Wargo MJ, Schneebeli ST, Li J. Aggregation State of Synergistic Antimicrobial Peptides. The Journal of Physical Chemistry Letters. 9501-9506. PMID 33108730 DOI: 10.1021/acs.jpclett.0c02094  0.592
2020 Sharafi M, McKay KT, Ivancic M, McCarthy DR, Dudkina N, Murphy KE, Rajappan SC, Campbell JP, Shen Y, Badireddy AR, Li J, Schneebeli ST. Size-selective Catalytic Polymer Acylation with a Molecular Tetrahedron. Chem. 6: 1469-1494. PMID 32728651 DOI: 10.1016/J.Chempr.2020.05.011  0.615
2020 Rajappan SC, McCarthy DR, Campbell JP, Ferrell JB, Sharafi M, Ambrozaite O, Li J, Schneebeli ST. Selective Monofunctionalization Enabled by Reaction History-Dependent Communication in Catalytic Rotaxanes. Angewandte Chemie (International Ed. in English). PMID 32525593 DOI: 10.1002/Anie.202006305  0.62
2019 Liao C, de Molliens MP, Schneebeli ST, Brewer M, Song G, Chatenet D, Braas KM, May V, Li J. Targeting the PAC1 Receptor for Neurological and Metabolic Disorders. Current Topics in Medicinal Chemistry. PMID 31284862 DOI: 10.2174/1568026619666190709092647  0.639
2019 Liao C, May V, Li J. Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics. Methods in Molecular Biology (Clifton, N.J.). 1947: 3-19. PMID 30969408 DOI: 10.1007/978-1-4939-9121-1_1  0.335
2019 Zhao X, Liao C, Ma YT, Ferrell JB, Schneebeli ST, Li J. A Top-Down Multiscale Approach to Simulate Peptide Self-Assembly from Monomers. Journal of Chemical Theory and Computation. PMID 30677300 DOI: 10.1021/Acs.Jctc.8B01025  0.644
2019 Ferrell JB, Campbell JP, McCarthy DR, McKay KT, Hensinger M, Srinivasan R, Zhao X, Wurthmann A, Li J, Schneebeli ST. Chemical Exploration with Virtual Reality in Organic Teaching Laboratories Journal of Chemical Education. 96: 1961-1966. DOI: 10.1021/Acs.Jchemed.9B00036  0.619
2019 Campbell JP, Rajappan SC, Jaynes TJ, Sharafi M, Ma Y, Li J, Schneebeli ST. Inside Back Cover: Enantioselective Electrophilic Aromatic Nitration: A Chiral Auxiliary Approach (Angew. Chem. Int. Ed. 4/2019) Angewandte Chemie International Edition. 58: 1219-1219. DOI: 10.1002/Anie.201814097  0.62
2018 Campbell JP, Rajappan SC, Jaynes TJ, Sharafi M, Ma YT, Li J, Schneebeli ST. Enantioselective Electrophilic Aromatic Nitration - A Chiral Auxiliary Approach. Angewandte Chemie (International Ed. in English). PMID 30402995 DOI: 10.1002/Anie.201811517  0.644
2018 Heppner DE, Dustin CM, Liao C, Hristova M, Veith C, Little AC, Ahlers BA, White SL, Deng B, Lam YW, Li J, van der Vliet A. Direct cysteine sulfenylation drives activation of the Src kinase. Nature Communications. 9: 4522. PMID 30375386 DOI: 10.1038/S41467-018-06790-1  0.307
2018 Liao C, May V, Li J. PAC1 Receptors: Shapeshifters in Motion. Journal of Molecular Neuroscience : Mn. PMID 30074173 DOI: 10.1007/S12031-018-1132-0  0.312
2018 Campbell JP, Rajappan SC, Jaynes TJ, Sharafi M, Ma Y, Li J, Schneebeli ST. Innenrücktitelbild: Enantioselective Electrophilic Aromatic Nitration: A Chiral Auxiliary Approach (Angew. Chem. 4/2019) Angewandte Chemie. 131: 1231-1231. DOI: 10.1002/Ange.201814097  0.618
2017 Liao C, Zhao X, Brewer M, May V, Li J. Conformational Transitions of the Pituitary Adenylate Cyclase-Activating Polypeptide Receptor, a Human Class B GPCR. Scientific Reports. 7: 5427. PMID 28710390 DOI: 10.1038/S41598-017-05815-X  0.318
2017 Shelley MY, Selvan ME, Zhao J, Babin V, Liao C, Li J, Shelley JC. A new mixed all-atom/coarse-grained model: application to melittin aggregation in aqueous solution. Journal of Chemical Theory and Computation. PMID 28636825 DOI: 10.1021/Acs.Jctc.7B00071  0.325
2017 Sharafi M, Campbell JP, Rajappan SC, Dudkina N, Gray DL, Woods TJ, Li J, Schneebeli ST. Crystal-Packing-Driven Enrichment of Atropoisomers. Angewandte Chemie (International Ed. in English). PMID 28510353 DOI: 10.1002/Anie.201701876  0.631
2017 Murphy KE, Bocanegra JL, Liu X, Chau HK, Lee PC, Li J, Schneebeli ST. Precise through-space control of an abiotic electrophilic aromatic substitution reaction. Nature Communications. 8: 14840. PMID 28378788 DOI: 10.1038/Ncomms14840  0.626
2017 Liao C, Zhao X, Liu J, Schneebeli ST, Shelley JC, Li J. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models. Physical Chemistry Chemical Physics : Pccp. PMID 28317993 DOI: 10.1039/C7Cp00200A  0.638
2017 Madsen JJ, Sinitskiy AV, Li J, Voth GA. Highly Coarse-grained Representations of Transmembrane Proteins. Journal of Chemical Theory and Computation. PMID 28043122 DOI: 10.1021/Acs.Jctc.6B01076  0.315
2017 Shelley JC, Shelley M, Esai Selvan M, Zhao J, Babin V, Liao C, Li J. Studying Peptide Aggregation using Mixed All-Atom/Coarse Grain Molecular Dynamics Simulations Biophysical Journal. 112: 198a. DOI: 10.1016/J.Bpj.2016.11.1096  0.323
2016 Liao C, Zhang Z, Kale J, Andrews DW, Lin J, Li J. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation. Scientific Reports. 6: 29502. PMID 27381287 DOI: 10.1038/Srep29502  0.318
2016 Tian W, Zeng C, An Y, Wang C, Liu Y, Li J. Accuracy and postoperative assessment of pedicle screw placement during scoliosis surgery with computer-assisted navigation: a meta-analysis. The International Journal of Medical Robotics + Computer Assisted Surgery : Mrcas. PMID 26957362 DOI: 10.1002/rcs.1732  0.384
2016 Sharafi M, Weinert ZJ, Cohen IM, Liao C, Ivancic M, Li J, Schneebeli ST. Controlled Self-Assembly inside C-Shaped Polyaromatic Strips Synlett. 27: 2145-2149. DOI: 10.1055/S-0035-1561479  0.656
2015 Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis. Angewandte Chemie (International Ed. in English). 54: 12772-6. PMID 26349630 DOI: 10.1002/Anie.201506793  0.648
2015 Liao C, Esai Selvan M, Zhao J, Slimovitch JL, Schneebeli ST, Shelley M, Shelley JC, Li J. Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 26208115 DOI: 10.1021/Acs.Jpcb.5B03254  0.633
2015 Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Inside Cover: Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis (Angew. Chem. Int. Ed. 43/2015) Angewandte Chemie International Edition. 54: 12518-12518. DOI: 10.1002/Anie.201508443  0.637
2015 Liu X, Weinert ZJ, Sharafi M, Liao C, Li J, Schneebeli ST. Innentitelbild: Regulating Molecular Recognition with C-Shaped Strips Attained by Chirality-Assisted Synthesis (Angew. Chem. 43/2015) Angewandte Chemie. 127: 12700-12700. DOI: 10.1002/Ange.201508443  0.637
2014 Li J, Ziemba BP, Falke JJ, Voth GA. Interactions of protein kinase C-α C1A and C1B domains with membranes: a combined computational and experimental study. Journal of the American Chemical Society. 136: 11757-66. PMID 25075641 DOI: 10.1021/Ja505369R  0.334
2014 Bruns CJ, Li J, Frasconi M, Schneebeli ST, Iehl J, Jacquot de Rouville HP, Stupp SI, Voth GA, Stoddart JF. An electrochemically and thermally switchable donor-acceptor [c2]daisy chain rotaxane. Angewandte Chemie (International Ed. in English). 53: 1953-8. PMID 24505012 DOI: 10.1002/Anie.201308498  0.632
2014 Li J, Jonsson A, Jakobtorweihen S, Shelley MY, Voth GA, Farid R, Shelley JC. Development of an All-Atom/Coarse Grain, Mixed Resolution Model for Proteins and their Environment Biophysical Journal. 106: 608a. DOI: 10.1016/J.Bpj.2013.11.3362  0.342
2013 Li J, Jonsson AL, Beuming T, Shelley JC, Voth GA. Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor. Journal of the American Chemical Society. 135: 8749-59. PMID 23678995 DOI: 10.1021/Ja404391Q  0.341
2011 Li J, Schneebeli ST, Bylund J, Farid R, Friesner RA. IDSite: An accurate approach to predict P450-mediated drug metabolism. Journal of Chemical Theory and Computation. 7: 3829-3845. PMID 22247702 DOI: 10.1021/Ct200462Q  0.73
2011 Zhao S, Zhu K, Li J, Friesner RA. Progress in super long loop prediction. Proteins. 79: 2920-35. PMID 21905115 DOI: 10.1002/Prot.23129  0.589
2011 Li J, Abel R, Zhu K, Cao Y, Zhao S, Friesner RA. The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins. 79: 2794-812. PMID 21905107 DOI: 10.1002/Prot.23106  0.684
2011 Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. Journal of the American Chemical Society. 133: 7384-97. PMID 21517016 DOI: 10.1021/Ja110287Y  0.494
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