Publications

Structural modeling and experimental validation define the MxA-Thogotovirus nucleoprotein interface that drives restriction and escapePreprint

LA Chi, ME Levy, RA Geiger, HS Malik, JS Patel

bioRxiv

DOI

Predicting color vision from visual opsin sequence with interpretable machine learningPresentation

F Sotelo, SK Pandey, JS Patel

Idaho Conference on Undergraduate Research

A comprehensive structural and functional analysis of Saccharomyces killer toxins

JW Creagh, LL Givens, DC Reetz, SA Coss, R Bizarria Jr, SA Alias, et al.

Toxins 18(5):235

DOIPubMed 42188637

Leveraging neural networks to correct FoldX free energy estimates

JE Barnes, LA Chi, SK Pandey, FM Ytreberg, JS Patel

ACS Omega

DOIPubMed 42222805

A constrained degron tag engineered to enhance auxin-inducible protein degradation

Z Han, A Alkhadrawi, S Tofani, W Zhang, LA Chi, J Maruwan, JS Patel, et al.

ACS Synthetic Biology 15(4):1577–1587

DOIPubMed 41941339

Leveraging neural networks to correct FoldX free-energy estimatesAbstract

LA Chi, J Barnes, S Pandey, FM Ytreberg, J Patel

Biophysical Journal 125(4):36a

DOI

Unraveling spectral shifts in microbial rhodopsin through machine learning predictions and molecular dynamics simulationsAbstract

SK Pandey, A Naik, JS Patel

Biophysical Journal 125(4):336a

DOI

Deep-sea fish reveal an alternative developmental trajectory for vertebrate vision

LG Fogg, S Isari, JE Barnes, JS Patel, NJ Marshall, W Salzburger, et al.

Science Advances 12(7):eadx2596

DOIPubMed 41671374

The H5N1 escape playbook: from computational prediction to pandemic preparednessPresentation

S Lauer, J Patel, A Chi

Computational discovery of new fungicide candidates to protect potato cropsPresentation

J Keele, J Patel

The Saccharomyces killer toxin K62 is a protein of the aerolysin family

JW Creagh, M Rolfsmeier, KJ Evans, R Bizarria Jr, DC Reetz, TJ Badigian, et al.

mBio 16(12):e01425-25

DOIPubMed 41217184

ΦX174 bacteriophage viability predicted by protein biophysical modelingPreprint

JT Van Leuven, JS Patel, C Beard, FM Ytreberg, LA Scott, K Burns, et al.

bioRxiv

DOIPubMed 41573941

Modeling the relationship between the capsid spike protein stability and fitness in ϕX174 bacteriophagePreprint

Y Sapozhnikov, JT Van Leuven, JS Patel, CR Miller

bioRxiv

DOI

The identification of a novel interaction site for the human immunodeficiency virus capsid on nucleoporin 153

S Li, P Lund-Andersen, SH Wang, FM Ytreberg, MT Naik, JS Patel, et al.

Journal of General Virology 106(5):002104

DOIPubMed 40366356

Exploring the ability of the MD+FoldX method to predict SARS-CoV-2 antibody escape mutations using large-scale data

LA Chi, JE Barnes, JS Patel, FM Ytreberg

Scientific Reports 14(1):23122

DOIPubMed 39366988

Molecular mechanisms underlying the spectral shift in zebrafish cone opsinsPreprint

LA Chi, SK Pandey, W Kolodziejczyk, P Lund-Andersen, JE Barnes, et al.

bioRxiv

DOIPubMed 39386526

Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1

EL Bruger, ZT Hying, D Singla, NL Márquez Reyes, SK Pandey, JS Patel, et al.

Applied and Environmental Microbiology 90(7):e00310-24

DOIPubMed 38934615

Human milk protein-derived bioactive peptides from in vitro-digested colostrum exert antimicrobial activities against common neonatal pathogens

Y Lyu, BJ Kim, JS Patel, DC Dallas, Y Chen

Nutrients 16(13):2040

DOIPubMed 38999788

Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability

Y Sapozhnikov, JS Patel, FM Ytreberg, CR Miller

BMC Bioinformatics 24(1):426

DOIPubMed 37953256

Hot trends in computer-aided drug design techniques

L Scotti, JS Patel, M Hassanzadeh, MT Scotti

Frontiers in Cellular and Infection Microbiology 13:1149994

DOIPubMed 37139493

Interactions between digestion-released human milk peptides and cell surface receptors targeting inflammationAbstract

K Heckathorn, J Patel, Y Chen

Current Developments in Nutrition 7

DOI

The effect of mutations on binding interactions between the SARS-CoV-2 receptor binding domain and neutralizing antibodies B38 and CB6

JE Barnes, PK Lund-Andersen, JS Patel, FM Ytreberg

Scientific Reports 12(1):18819

DOIPubMed 36335244

Defining the HIV capsid binding site of nucleoporin 153

S Li, JS Patel, J Yang, AM Crabtree, BM Rubenstein, PK Lund-Andersen, et al.

mSphere 7(5):e00310-22

DOIPubMed 36040047

Molecular modeling predicts novel antibody escape mutations in the respiratory syncytial virus fusion glycoprotein

SS Beach, MKA Hull, FM Ytreberg, JS Patel, TA Miura

Journal of Virology 96(13):e00353-22

DOIPubMed 35678603

An evo-devo study of salmonid visual opsin dynamics and photopigment spectral sensitivity

M Eilertsen, WIL Davies, D Patel, JE Barnes, R Karlsen, JK Mountford, et al.

Frontiers in Neuroanatomy 16:945344

DOIPubMed 35899127

The characterization of a novel virus discovered in the yeast Pichia membranifaciens

MD Lee, JW Creagh, LR Fredericks, AM Crabtree, JS Patel, PA Rowley

Viruses 14(3):594

DOIPubMed 35337001

Paired simulations and experimental investigations into the calcium-dependent conformation of albumin

D Patel, SL Haag, JS Patel, FM Ytreberg, MT Bernards

Journal of Chemical Information and Modeling 62(5):1282

DOIPubMed 35194993

Determining the mechanism of a spectral shift in cone visual pigments using atomistic molecular simulationsAbstract

PK Lund-Andersen, FM Ytreberg, JS Patel

Biophysical Journal 121(3):44a–45a

DOI

Targeting SUMOylation dependency in human cancer stem cells through a unique SAE2 motif revealed by chemical genomics

YD Benoit, RR Mitchell, W Wang, L Orlando, AL Boyd, B Tanasijevic, et al.

Cell Chemical Biology 28(10):1394–1406

DOIPubMed 33979648

The pesticide chlorpyrifos promotes obesity by inhibiting diet-induced thermogenesis in brown adipose tissue

B Wang, EE Tsakiridis, S Zhang, A Llanos, EM Desjardins, JM Yabut, et al.

Nature Communications 12(1):5163

DOIPubMed 34453052

Nuku, a family of primate retrocopies derived from KU70

PA Rowley, A Ellahi, K Han, JS Patel, JT Van Leuven, SL Sawyer

G3 11(8):jkab163

DOIPubMed 34849803

EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde

JV Bazurto, DD Nayak, T Ticak, M Davlieva, JA Lee, CN Hellenbrand, et al.

PLOS Biology 19(5):e3001208

DOIPubMed 34038406

Implementing and assessing an alchemical method for calculating protein–protein binding free energy

D Patel, JS Patel, FM Ytreberg

Journal of Chemical Theory and Computation 17(4):2457

DOIPubMed 33709712

Assessment of software methods for estimating protein-protein relative binding affinities

TR Gonzalez, KP Martin, JE Barnes, JS Patel, FM Ytreberg

PLOS ONE 15(12):e0240573

DOIPubMed 33347442

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

D Patel, JE Barnes, WIL Davies, DL Stenkamp, JS Patel

PLOS Computational Biology 16(10):e1008212

DOIPubMed 33085657

Predicting the viability of beta-lactamase: how folding and binding free energies correlate with beta-lactamase fitness

J Yang, N Naik, JS Patel, CS Wylie, W Gu, J Huang, FM Ytreberg, MT Naik, et al.

PLOS ONE 15(5):e0233509

DOIPubMed 32470971

Electrostatic switching controls channel dynamics of the sensor protein VirB10 in A. tumefaciens type IV secretion system

VC Darbari, J Ciccone, JS Patel, B Islam, PK Agarwal, S Haider

ACS Omega 5(7):3271

DOIPubMed 32118142

Dynamic virtual proteins: visualization, interaction and collaboration in virtual reality

JM Gauthier, I McGrath, JS Patel

Proceedings of the 25th ACM Symposium on Virtual Reality Software and Technology

DOI

Vision using multiple distinct rod opsins in deep-sea fishes

Z Musilova, F Cortesi, M Matschiner, WIL Davies, JS Patel, SM Stieb, et al.

Science 364(6440):588–592

DOIPubMed 31073066

Expanding the watch list for potential Ebola virus antibody escape mutations

JS Patel, CJ Quates, EL Johnson, FM Ytreberg

PLOS ONE 14(3):e0211093

DOIPubMed 30897171

Calculation of protein-protein binding free energies using umbrella sampling with dual resolution water modelsAbstract

JS Patel, FM Ytreberg

Biophysical Journal 116(3):291a

DOI

Fast calculation of protein–protein binding free energies using umbrella sampling with a coarse-grained model

JS Patel, FM Ytreberg

Journal of Chemical Theory and Computation 14(2):991–997

DOIPubMed 29286646

Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations

JS Patel, CJ Brown, FM Ytreberg, DL Stenkamp

PLOS Computational Biology 14(1):e1005974

DOIPubMed 29364888

Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression

A González-González, SM Hug, A Rodríguez-Verdugo, JS Patel, BS Gaut

Molecular Biology and Evolution 34(11):2839–2855

DOIPubMed 28961910

Steered molecular dynamics simulations for studying protein–ligand interaction in cyclin-dependent kinase 5

JS Patel, A Berteotti, S Ronsisvalle, W Rocchia, A Cavalli

Journal of Chemical Information and Modeling 54(2):470–480

DOIPubMed 24437446

Insights into protein-ligand binding using enhanced sampling methodsDissertation

JS Patel

Ph.D. dissertation

Elucidating the binding behavior of highly potent COX-2 selective inhibitors

FS Di Leva, JS Patel, V Limongelli, D Branduardi, L Marinelli, E Novellino, et al.

Insights into ligand–protein binding from local mechanical response

JS Patel, D Branduardi, M Masetti, W Rocchia, A Cavalli

Journal of Chemical Theory and Computation 7(10):3368

DOIPubMed 22003321

Molecular modeling on inhibitor complexes and active-site dynamics of cytochrome P450 C17, a target for prostate cancer therapy

SM Haider, JS Patel, CS Poojari, S Neidle

Journal of Molecular Biology 400(5):1078–1098

DOIPubMed 20595043