Click on an image to see a larger version.
†denotes corresponding author *denotes co-first author

Purdue publications
(2016 - Present)


Identification of monomethyl branched chain lipids by a combination of liquid chromatography tandem mass spectrometry and charge-switching chemistries

Randolph C, Beveridge C, Iyer S, Blanksby S, McLuckey S, Chopra G

JASMS (2022) 




Neurotoxic reactive astrocytes induce cell death via saturated lipids

Guttenplan K, Weigel MK, Prakash P, Wijewardhane PR, Hasel P, Rufen-Blanchette U, Münch AE, Blum
JA, Fine J, Neal M, Bruce KD, Gitler AD, Chopra G, Liddelow SA, Barres B.  

Nature (2021) 





Automated Bioanalytical Workflow for Ligand Binding Based Pharmacokinetic Assay Development
Evans B, Yeung L, Beck A, Li A, Lee DH, Chopra G†, Bateman K.† 



Learning relationships between chemical and physical stability for drug development
Fine JA, Wijewardhane PR, Dawood S, Smith K, Bothe J, Krishnamachari Y, Andrews A, Wuefling P, Liu Y, Chopra G†.




Accurate Prediction of Inhibitor Binding to HIV-1 Protease using CANDOCK

Falls Z, Fine J, Chopra G, Samudrala R.

Fronteirs in Chemistry (2021) 

[Fronteirs in Chemistry]


One Scaffold – Different Organelles Sensors: pH-Activable Fluorescent Probes for Targeting Live Primary Microglial Cell Organelles
Jethava KP*, Prakash P*, Manchanda P, Arora H, Chopra G†.
ChemBioChem (2021)




Monitoring phagocytic uptake of amyloid β into glial cell lysosomes in real time

Prakash P*, Jethava KP*, Korte N*, Izquierdo P*, Favuzzi E, Rose IVL, Guttenplan KA, Manchanda P, Dutta S, Rochet J-C, Fishell G, Liddelow S, Attwell DChopra G

Chem. Sci., 2021,12, 10901-10918

[Chemical Science]



Graph based machine learning interprets and predicts diagnostic isomer-selective ion-molecule reactions in tandem mass spectrometry.
Fine J, Li JK-Y*, Beck A, Alzarieni K, Ma X, Boulos V, Kenttämaa HI, Chopra G

Chem. Sci. 11, 11849-11858 (2020).

[Chemical Science]



Accelerated reactivity mechanism and interpretable machine learning model of N-Sulfonylimines towards fast multicomponent reactions
Jethava KP, Fine JA, Chen Y, Hossain A, Chopra G
Org. Lett. 22, 21, 8480–8486 (2020).

[Organic Letters]

[Reaction Mechanism]



A 2‐Tyr‐1‐Carboxylate Mononuclear Iron Center is the Active Site of Dimethylformamidase
Arya CK, Yadav S, Fine J, Casanal A, Chopra G, Ramanathan G, Vinothkumar KR, Subramanian R.

Angew Chemie. Int. Ed. 59, 39, 16961-16966 (2020).

[Angew Chemie. Int. Ed.]



Spectral Deep Learning for Prediction and Prospective Validation of Functional Groups
Fine J, Rasjashekar A*, Jethava K,Chopra G† 

Chem. Sci. 11, 4618-4630 (2020).



Targeting polyamine biosynthesis to stimulate beta cell regeneration in zebrafish
Robertson M ,Padgett L, Fine J, Chopra G, Mastracci T 

Islets. Sep 2;12(5):99-107 (2020).



jcisd8.2020.60.issue-9.largecover.jpg Open source software for analyzing large scale drug-protein-disease data.
Mangione W, Falls Z, Chopra G, Samudrala R
J. Chem. Inf. Model. 60, 9, 4131-4136 (2020).




DUBS: A framework for developing Directory of Useful Benchmarking Sets for virtual screening.
Fine J, Muhoberac M, Fraux G, Chopra G

J. Chem. Inf. Model. 60, 9, 4137-4143 (2020).




Shotgun Drug Repurposing Biotechnology to Tackle Epidemics and Pandemics
Mangione W, Falls Z, Melendy T, Chopra GSamudrala R

Drug Discovery Today. 25, 7, 1126-1128 (2020).

[Drug Discovery Today]



CANDOCK: Chemical atomic network based hierarchical flexible docking algorithm using generalized statistical potentials 
Fine J, Konc J, Samudrala R, Chopra G

J. Chem. Inf. Model. 2020, 60, 3, 1509-1527 (2020).



Integration of Biodynamic Imaging and RNA-seq classifies chemotherapy response in canine diffuse large B-cell lymphoma
Fine JA, Utturkar S, Dhawan D, San Miguel P, Chopra G, Turek J, Nolte D, Childress MO, Lanman NA. 




Graph Neural Networks Bootstrapped for Synthetic Selection and Validation of Small Molecule Immunomodulators
Wijewardhane PR, Jethava KP, Fine JA, Chopra G




Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications 
Fine J, Lackner R, Samudrala R, Chopra G

Scientific Reports, 9:13155 (2019).

[Scientiffic Reports]



Integrated pan-cancer map of EBV-associated neoplasms reveals functional host-virus interactions
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

Cancer Research. 79, 23, 6010-6023 (2019).  
1Integrated  pan-cancer  map  of  EBV-associated  neoplasms  reveals functional host-virus interactions


Rapid, Refined, and Robust Method for Expression, Purification, and Characterization of Recombinant Human Amyloid-beta M1-42 
Prakash P, Lantz TC, Jethava K, Chopra G

Methods Protoc. 20192(2), 48 (2019).



Lemon: a framework for rapidly mining structural information from the Protein Data Bank 
Fine J, Chopra G

Bioinformatics, 35(20): 4165–4167 (2019).


DOI: btz178



Molecular Interactions Using New Technology: A Virtual Reality Gaming Platform to Visualize and Manipulate Molecules
Zhang W, Fine J*, Sculley C, McGraw J, Chopra G

[ChemRxiv] [YouTube] [Abstract]


Stable and Reversible Functionalization and Super-Resolution Microscopy of Live Cell Membranes 
Hossain A, Majumder J, Bi C, Huang F, Chopra G


An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 
Keasar C, McGuffin LJ, Wallner B, Chopra G, et. al.

Scientific Reports, 2018, 8:9939 (2018).



Inhibition of 12/15-lipoxygenase protects against ß cell oxidative stress and glycemic deterioration in mouse models of type 1 diabetes.
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.
Diabetes, 2017, [Epub ahead of print] 
PMID: 28842399



Aminoisoquinoline benzamides, FLT3 and Src-family kinase inhibitors, potently inhibit proliferation of acute myeloid leukemia cell lines
Larocque E, Naganna N, Ma X, Opoku-Temeng C, Carter-Cooper B, Chopra G, Lapidus RG, Sintim HO.
Future Med Chem, 2017, 9(11)1213-1225



Identification of new FLT3 inhibitors that potently inhibit AML cell lines, via an azo click-it/staple-it approach
Zhou J, Ma X, Wang C, Carter-Cooper B, Larocque, E, Fine J,
Tsuji G, Yang F, Chopra G, Lapidus RG, Sintim HO*.
ACS Med Chem Lett, 2017, 8 (5), 492–497
PMID: 28523099


New FLT3 Inhibitors That Potently Inhibit AML Cell.jpg


Combating Ebola with Repurposed Therapeutics Using the CANDO Platform
Chopra G†, Kaushik S, Elkin PL, Samudrala R
Molecules, 2016, 21(12): 1537


Summary: With the use of the CANDO platform and in vitro data, a significant reduction in time, risk, cost, and resources was shown when identifying drug leads for future Ebola outbreaks compared to tradition methods.

Combating Ebola with Repurposed Therapeutics Using the CANDO Platform.png


CD28 Costimulation: From Mechanism to Therapy
Esensten JH, Helou YA, Chopra G, Weiss A, Bluestone JA
Immunity, 2016, 44(5): 973-988
PMID: 27192564


Summary: This paper summarizes the current understanding of complex costimulatory pathways, including the individual roles of the CD28, B7-1/CD80, and B7-2/CD86 molecules.

CD28 costimulation from mechanism to therapy.jpg


Exploring polypharmacology in drug discovery and repurposing using the CANDO platform
Chopra G†, Samudrala R
Current Pharmaceutical Design, 2016, 22(21):3109-23
PMID: 27013226


Summary: Shows how the CANDO platform can be used to analyze and determine the contribution of multitargeting based approach (polypharmacology) to drug repurposing.

Exploring Polypharmacology in Drug Discovery and Repurposing.jpg

Stanford and UCSF publications
(2008 - 2015)


Divergent phenotypes of human regulatory T cells expressing the receptors TIGIT and CD226
Fuhrman CA, Yeh W-I, 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, Atkinson MA, Bluestone JA, Brusko TM
Immunology, 2015, 195(1): 145-155
PMID: 25994968


Summary: A set of studies elucidating functionally distinct regulatory T-cell subsets that may help direct cellular therapies and provide important phenotypic markers for assessing the role of Tregs in health and disease.

Divergent phenotypes of human regulatory T cells expressing the receptors TIGIT and CD2261.jpg


Multiscale modeling of relationships between protein classes and drug behavior across all diseases using the CANDO platform
Sethi G*, Chopra G*, Samudrala R
Medicinal Chemistry, 2015, 15(8): 705-17
PMID: 25694071


Summary: Uses the CANDO platform to analyze the interaction signatures between human approved compounds and the druggable proteome to determine drug behavior for different indications/diseases.

Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform.png


The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T-cell identity
DuPage M, Chopra G, Quiros J, Rosenthal WL, Morar MM, Holohan D, Zhang R, Turka L, Marson A, Bluestone JA
Immunity, 2015, 42(2): 227-38
PMID: 25680271


Summary: Chromatin-modifying enzyme along with CD28 costimulation are crucial for the maintenance of Treg cell identity during cellular activation.

The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T-cell identity.jpg


Oxido-reductive regulation of human vascular remodeling by the orphan receptor tyrosine kinase ROS1
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, Kuchinsky A, Channon K, Charest A, Quertermous T, Ashley EA
J. Clinical Investigation, 2014, 124(12): 5159-74
PMID: 25401476


Summary: This study indicates that glutathione peroxidase-1 (GPX1)-dependent alterations in oxido-reductive stress promote ROS1 activation and mediate vascular remodeling.

Oxido-reductive regulation of human vascular remodeling by the orphan receptor tyrosine kinase ROS1.jpg


CANDO and the infinite drug discovery frontier
Minie ME*, Chopra G*, Sethi G, Horst JA, Roy A, White G, Samudrala R
Drug Discovery Today, 2014, 19(9):1353-63
PMID: 24980786

[PDF]Summary: The Computational Analysis of Novel Drug Opportunities (CANDO) platform ( uses similarity of compound-proteome interaction signatures to infer homology of compound/drug behavior.

CANDO and the infinite drug discovery frontier.jpg


WeFold: Large-scale Coopetition for Protein Structure Prediction
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, et. al.
Proteins, 2014, 82(9):1850-1868


Summary: This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative.



Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin
Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S
PLoS One, 2013, 8(9): e74053
PMID: 24023924


Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic.png


Strategic protein target analysis for developing drugs to stop dental caries
Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JDB
Adv. Dent. Res., 2012, 24(2): 86-93
PMID: 22899687


Summary: The entire Streptococcus mutans proteome was analyzed for potential drug targets by investigating their uniqueness with respect to non-cariogenic dental plaque bacteria, quality of protein structure models, and the likelihood of finding a drug for the active si

Strategic protein target analysis for developing drugs to stop dental caries.jpg


KOBAMIN – KnOwledge BAsed MINimization server for protein structure refinement
Rodrigues J, Levitt M and Chopra G
Nucleic Acid Research, 2012, Web Server Issue. 40 (W1): W323-W328
PMCID: PMC3394243


Summary: The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force.

knowledge-based minimization web server for protein structure refinement.jpg


Remarkable patterns of surface water ordering around polarized buckminsterfullerene
Chopra G† and Levitt M
Proc. Natl. Acad. Sci. U.S.A., 2011, 108(35):14455-14460
PMID: 21844369


Summary: Molecular Dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3) shows that polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range.

Remarkable patterns of surface water ordering around polarized buckminsterfullerene1.jpg


Consistent refinement of submitted models at CASP using a knowledge-based potential
Chopra G†, Kalisman N, Levitt M
Proteins, 2010, 78(12): 2668-2678


Consistent refinement of submitted models at CASP using a knowledge-based potential.jpg


Solvent dramatically affects protein structure refinement
Chopra G, Summa CM, Levitt M
Proc. Natl. Acad. Sci. U.S.A., 2008, 105(51): 20239-20244
PMID: 19073921


Solvent dramatically affects protein structure refinement.jpg