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Gaurav Chopra, Ph.D. - Publications

Affiliations: 
2016- Chemistry, Drug Discovery, Cancer Center, Immunology, Neuroscience Purdue University, West Lafayette, IN, United States 
Area:
Chemical and Cellular Immunology: Neuroimmunology, Cancer Immunology, Drug Discovery, Chemical Data Science, Computational Biology, Bioinformatics, Systems Pharmacology
Website:
http://www.chopralab.com
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54 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 Evans BR, Beck AG, Yeung L, Li A, Lee DH, Bateman KP, Chopra G. Automated Bioanalytical Workflow for Ligand Binding-Based Pharmacokinetic Assay Development. Analytical Chemistry. PMID 38156369 DOI: 10.1021/acs.analchem.3c04589  0.579
2023 Santhakumari PR, Dhanabalan K, Virani S, Hopf-Jannasch AS, Benoit JB, Chopra G, Subramanian R. Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins. Plos One. 18: e0280009. PMID 37384723 DOI: 10.1371/journal.pone.0280009  0.749
2023 Prakash P, Manchanda P, Paouri E, Bisht K, Sharma K, Wijewardhane PR, Randolph CE, Clark MG, Fine J, Thayer EA, Crockett A, Gasmi N, Stanko S, Prayson RA, Zhang C, ... ... Chopra G, et al. Amyloid β Induces Lipid Droplet-Mediated Microglial Dysfunction in Alzheimer's Disease. Biorxiv : the Preprint Server For Biology. PMID 37333071 DOI: 10.1101/2023.06.04.543525  0.711
2023 Fine J, Wijewardhane PR, Mohideen SDB, Smith K, Bothe JR, Krishnamachari Y, Andrews A, Liu Y, Chopra G. Learning Relationships Between Chemical and Physical Stability for Peptide Drug Development. Pharmaceutical Research. PMID 36797504 DOI: 10.1007/s11095-023-03475-3  0.746
2022 Randolph CE, Beveridge CH, Iyer S, Blanksby SJ, McLuckey SA, Chopra G. Identification of Monomethyl Branched-Chain Lipids by a Combination of Liquid Chromatography Tandem Mass Spectrometry and Charge-Switching Chemistries. Journal of the American Society For Mass Spectrometry. PMID 36218280 DOI: 10.1021/jasms.2c00225  0.73
2022 Falls Z, Fine J, Chopra G, Samudrala R. Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK. Frontiers in Chemistry. 9: 775513. PMID 35111726 DOI: 10.3389/fchem.2021.775513  0.672
2021 Guttenplan KA, Weigel MK, Prakash P, Wijewardhane PR, Hasel P, Rufen-Blanchette U, Münch AE, Blum JA, Fine J, Neal MC, Bruce KD, Gitler AD, Chopra G, Liddelow SA, Barres BA. Neurotoxic reactive astrocytes induce cell death via saturated lipids. Nature. PMID 34616039 DOI: 10.1038/s41586-021-03960-y  0.738
2021 Jethava KP, Prakash P, Manchanda P, Arora H, Chopra G. One Scaffold - Different Organelle Sensors: pH-Activable Fluorescent Probes for Targeting Live Microglial Cell Organelles. Chembiochem : a European Journal of Chemical Biology. PMID 34585478 DOI: 10.1002/cbic.202100378  0.752
2021 Prakash P, Jethava KP, Korte N, Izquierdo P, Favuzzi E, Rose IVL, Guttenplan KA, Manchanda P, Dutta S, Rochet JC, Fishell G, Liddelow SA, Attwell D, Chopra G. Monitoring phagocytic uptake of amyloid β into glial cell lysosomes in real time. Chemical Science. 12: 10901-10918. PMID 34476070 DOI: 10.1039/d1sc03486c  0.758
2020 Fine JA, Rajasekar AA, Jethava KP, Chopra G. Spectral deep learning for prediction and prospective validation of functional groups. Chemical Science. 11: 4618-4630. PMID 34122917 DOI: 10.1039/c9sc06240h  0.763
2020 Fine J, Kuan-Yu Liu J, Beck A, Alzarieni KZ, Ma X, Boulos VM, Kenttämaa HI, Chopra G. Graph-based machine learning interprets and predicts diagnostic isomer-selective ion-molecule reactions in tandem mass spectrometry. Chemical Science. 11: 11849-11858. PMID 34094414 DOI: 10.1039/d0sc02530e  0.765
2020 Jethava KP, Fine J, Chen Y, Hossain A, Chopra G. Accelerated Reactivity Mechanism and Interpretable Machine Learning Model of -Sulfonylimines toward Fast Multicomponent Reactions. Organic Letters. PMID 33074678 DOI: 10.1021/acs.orglett.0c03083  0.758
2020 Robertson MA, Padgett LR, Fine JA, Chopra G, Mastracci TL. Targeting polyamine biosynthesis to stimulate beta cell regeneration in zebrafish. Islets. 1-9. PMID 32715853 DOI: 10.1080/19382014.2020.1791530  0.584
2020 Fine J, Muhoberac M, Fraux G, Chopra G. DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening. Journal of Chemical Information and Modeling. PMID 32639154 DOI: 10.1021/Acs.Jcim.0C00122  0.711
2020 Mangione W, Falls Z, Chopra G, Samudrala R. cando.py: Open source software for predictive bioanalytics of large scale drug-protein-disease data. Journal of Chemical Information and Modeling. PMID 32515949 DOI: 10.1021/Acs.Jcim.0C00110  0.625
2020 Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R. Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Chemrxiv : the Preprint Server For Chemistry. PMID 32511286 DOI: 10.26434/chemrxiv.12045318  0.545
2020 Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R. A 2-Tyr-1-Carboxylate Mononuclear Iron Center is the Active Site of Dimethylformamidase. Angewandte Chemie (International Ed. in English). PMID 32452120 DOI: 10.1002/Anie.202005332  0.582
2020 Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R. Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Drug Discovery Today. PMID 32405249 DOI: 10.1016/J.Drudis.2020.05.002  0.584
2020 Fine J, Konc J, Samudrala R, Chopra G. CANDOCK: Chemical Atomic Network-based Hierarchical Flexible Docking Algorithm using Generalized Statistical Potentials. Journal of Chemical Information and Modeling. PMID 32069042 DOI: 10.1021/Acs.Jcim.9B00686  0.703
2020 Fine JA, Rajasekar AA, Jethava KP, Chopra G. Spectral deep learning for prediction and prospective validation of functional groups Chemical Science. 11: 4618-4630. DOI: 10.1039/C9Sc06240H  0.764
2020 Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R. A 2‐Tyr‐1‐Carboxylate Mononuclear Iron Center is the Active Site of Dimethylformamidase Angewandte Chemie. DOI: 10.1002/Ange.202005332  0.55
2019 Fine J, Lackner R, Samudrala R, Chopra G. Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Scientific Reports. 9: 13155. PMID 31511563 DOI: 10.1038/S41598-019-49515-0  0.694
2019 Chakravorty S, Yan B, Wang C, Wang L, Quaid JT, Lin CF, Briggs SD, Majumder J, Canaria DA, Chauss D, Chopra G, Olson MR, Zhao B, Afzali B, Kazemian M. Integrated pan-cancer map of EBV-associated neoplasms reveals functional host-virus interactions. Cancer Research. PMID 31481499 DOI: 10.1158/0008-5472.Can-19-0615  0.648
2019 Prakash P, Lantz TC, Jethava KP, Chopra G. Rapid, Refined, and Robust Method for Expression, Purification, and Characterization of Recombinant Human Amyloid beta 1-42. Methods and Protocols. 2. PMID 31181684 DOI: 10.3390/mps2020048  0.77
2019 Fine J, Chopra G. Lemon: a framework for rapidly mining structural information from the Protein Data Bank. Bioinformatics (Oxford, England). PMID 30873531 DOI: 10.1093/Bioinformatics/Btz178  0.595
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.465
2018 Majumder J, Fine JA, Lantz TC, Conder CJ, Chopra G. Abstract LB-076: Cancer cell specific lethality by degrading specific protein target network identified using a chemical screening based machine learning method Cancer Research. 78. DOI: 10.1158/1538-7445.Am2018-Lb-076  0.678
2018 Kischuk E, Majumder J, Fine JA, Lantz TC, Dhawan D, Knapp DW, Ratliff TL, Chopra G. Abstract 4709: Cell-specific gene program-based small-molecule immunomodulators targeting solid-tumor microenvironments Cancer Research. 78: 4709-4709. DOI: 10.1158/1538-7445.Am2018-4709  0.744
2018 Fine JA, Chopra G. CANDOCK: Conformational Entropy Driven Analytics for Class-Specific Proteome-Wide Docking Biophysical Journal. 114: 57a. DOI: 10.1016/J.Bpj.2017.11.363  0.587
2018 Chopra G. Targeting Proteome-Scale Networks to Design and Synthesize Potent Anticancer and Cell-Specific Immunomodulatory Compounds Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.3577  0.377
2018 Majumder J, Chopra G. Live Cell Surface Conjugation Methods for Imaging, Sensing and Therapy Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.154  0.626
2018 McGraw J, Zhang W, Luginbuhl AD, Takahashi G, Tasker RF, Chopra G. Virtual Reality Environment to Visualize and Manipulate Molecular Structures Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1029  0.327
2017 Hernandez-Perez M, Chopra G, Fine J, Conteh AM, Anderson RM, Linnemann AK, Benjamin C, Nelson JB, Benninger KS, Nadler JL, Maloney DJ, Tersey SA, Mirmira RG. Inhibition of 12/15-Lipoxygenase Protects Against β Cell Oxidative Stress and Glycemic Deterioration in Mouse Models of Type 1 Diabetes. Diabetes. PMID 28842399 DOI: 10.2337/Db17-0215  0.595
2017 Ma X, Zhou J, Wang C, Carter-Cooper B, Yang F, Larocque E, Fine J, Tsuji G, Chopra G, Lapidus RG, Sintim HO. Identification of New FLT3 Inhibitors That Potently Inhibit AML Cell Lines via an Azo Click-It/Staple-It Approach. Acs Medicinal Chemistry Letters. 8: 492-497. PMID 28523099 DOI: 10.1021/Acsmedchemlett.6B00468  0.58
2017 Larocque E, Naganna N, Ma X, Opoku-Temeng C, Carter-Cooper B, Chopra G, Lapidus RG, Sintim HO. Aminoisoquinoline benzamides, FLT3 and Src-family kinase inhibitors, potently inhibit proliferation of acute myeloid leukemia cell lines. Future Medicinal Chemistry. PMID 28490193 DOI: 10.4155/Fmc-2017-0067  0.331
2017 Majumder J, Lantz T, Fine J, Chopra G. Abstract A35: Drug repurposing for castration resistant prostate cancer based on disease-disease relationships Cancer Research. 77. DOI: 10.1158/1538-7445.Transcontrol16-A35  0.743
2016 Chopra G, Kaushik S, Elkin PL, Samudrala R. Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Molecules (Basel, Switzerland). 21. PMID 27898018 DOI: 10.3390/Molecules21121537  0.624
2016 Esensten JH, Helou YA, Chopra G, Weiss A, Bluestone JA. CD28 Costimulation: From Mechanism to Therapy. Immunity. 44: 973-88. PMID 27192564 DOI: 10.1016/J.Immuni.2016.04.020  0.51
2016 Chopra G, Samudrala R. Exploring polypharmacology in drug discovery and repurposing using the CANDO platform. Current Pharmaceutical Design. PMID 27013226 DOI: 10.2174/1381612822666160325121943  0.612
2015 Fuhrman CA, Yeh WI, Seay HR, Saikumar Lakshmi P, Chopra G, Zhang L, Perry DJ, McClymont SA, Yadav M, Lopez MC, Baker HV, Zhang Y, Li Y, Whitley M, von Schack D, et al. Divergent Phenotypes of Human Regulatory T Cells Expressing the Receptors TIGIT and CD226. Journal of Immunology (Baltimore, Md. : 1950). 195: 145-55. PMID 25994968 DOI: 10.4049/Jimmunol.1402381  0.651
2015 Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Mini Reviews in Medicinal Chemistry. 15: 705-17. PMID 25694071 DOI: 10.2174/1389557515666150219145148  0.631
2015 DuPage M, Chopra G, Quiros J, Rosenthal WL, Morar MM, Holohan D, Zhang R, Turka L, Marson A, Bluestone JA. The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T cell identity after activation. Immunity. 42: 227-38. PMID 25680271 DOI: 10.1016/J.Immuni.2015.01.007  0.527
2015 Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform Mini-Reviews in Medicinal Chemistry. 15: 705-717. DOI: 10.4172/0974-276X.C1.079  0.564
2015 Fuhrman CA, Yeh WI, Seay HR, Lakshmi PS, Chopra G, Zhang L, Perry DJ, McClymont SA, Yadav M, Lopez MC, Baker HV, Zhang Y, Li Y, Whitley M, Von Schack D, et al. Divergent phenotypes of human regulatory T cells expressing the receptors TIGIT and CD226 Journal of Immunology. 195: 145-155. DOI: 10.4049/jimmunol.1402381  0.614
2014 Ali ZA, de Jesus Perez V, Yuan K, Orcholski M, Pan S, Qi W, Chopra G, Adams C, Kojima Y, Leeper NJ, Qu X, Zaleta-Rivera K, Kato K, Yamada Y, Oguri M, et al. Oxido-reductive regulation of vascular remodeling by receptor tyrosine kinase ROS1. The Journal of Clinical Investigation. 124: 5159-74. PMID 25401476 DOI: 10.1172/Jci77484  0.356
2014 Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. Drug Discovery Today. 19: 1353-63. PMID 24980786 DOI: 10.1016/J.Drudis.2014.06.018  0.633
2014 Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, et al. WeFold: a coopetition for protein structure prediction. Proteins. 82: 1850-68. PMID 24677212 DOI: 10.1002/Prot.24538  0.527
2013 Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S. Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin. Plos One. 8: e74053. PMID 24023924 DOI: 10.1371/Journal.Pone.0074053  0.605
2013 Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska M, Sieradzan A, Smadbeck J, et al. Wefold: A collaborative protein structure prediction experiment Computational Molecular Science and Engineering Forum 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 182-184.  0.439
2012 Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. Strategic protein target analysis for developing drugs to stop dental caries. Advances in Dental Research. 24: 86-93. PMID 22899687 DOI: 10.1177/0022034512449837  0.629
2012 Rodrigues JP, Levitt M, Chopra G. KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Research. 40: W323-8. PMID 22564897 DOI: 10.1093/Nar/Gks376  0.535
2011 Chopra G, Levitt M. Remarkable patterns of surface water ordering around polarized buckminsterfullerene. Proceedings of the National Academy of Sciences of the United States of America. 108: 14455-60. PMID 21844369 DOI: 10.1073/Pnas.1110626108  0.482
2010 Chopra G, Kalisman N, Levitt M. Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins. 78: 2668-78. PMID 20589633 DOI: 10.1002/Prot.22781  0.525
2008 Chopra G, Summa CM, Levitt M. Solvent dramatically affects protein structure refinement. Proceedings of the National Academy of Sciences of the United States of America. 105: 20239-44. PMID 19073921 DOI: 10.1073/Pnas.0810818105  0.512
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