Publications

2025

Journal Articles

Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks

K-Y. M. Chen; J. K. Lai; L. S. P. Rudden; J. Wang; A. M. Russell et al. 

Nature Chemistry. 2025. DOI : 10.1038/s41557-024-01719-2.

Reviews

Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery

P. Conflitti; E. Lyman; M. S. Sansom; P. W. Hildebrand; H. Gutiérrez-de-Terán et al. 

Nature Reviews Drug Discovery. 2025. DOI : 10.1038/s41573-024-01083-3.

Theses

Molecular characterization of an adhesion GPCR signal transduction using Graph-neural networks

M. F. Marfoglia / P. Barth (Dir.)  

Lausanne, EPFL, 2025. 

2024

Journal Articles

Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations

J. Bender; T. Kundlacz; L. S. P. Rudden; M. Frick; J. Bieber et al. 

STRUCTURE. 2024. Vol. 32, num. 10. DOI : 10.1016/j.str.2024.07.017.

Inducible CXCL12/CXCR4–dependent extramedullary hematopoietic niches in the adrenal gland

F. Schyrr; A. Alonso-Calleja; A. Vijaykumar; J. Sordet-Dessimoz; S. Gebhard et al. 

Blood. 2024. Vol. 144, num. 9, p. 964 – 976. DOI : 10.1182/blood.2023020875.

Unravelling the components of diffuse scattering using deep learning

C. A. Fuller; L. S. P. Rudden 

Iucrj. 2024. Vol. 11, p. 34 – 44. DOI : 10.1107/S2052252523009521.

Antibodies expand the scope of angiotensin receptor pharmacology

M. A. Skiba; S. M. Sterling; S. Rawson; S. Zhang; H. Xu et al. 

Nature Chemical Biology. 2024. DOI : 10.1038/s41589-024-01620-6.

Theses

Boosting CAR T-cell therapy through G-protein signal rewiring

L. Y. Smeding / P. Barth (Dir.)  

Lausanne, EPFL, 2024. 

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

M. Hijazi / P. D. Barth (Dir.)  

Lausanne, EPFL, 2024. 

Working Papers

AlloPool: An Adaptive Graph Neural Network for Dynamic Allosteric Network Prediction in Protein Systems

M. F. Marfoglia; L. Guirardel; P. Barth 

2024

2023

Journal Articles

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

R. Jefferson; A. Oggier; A. Füglistaler; N. Camviel; M. Hijazi et al. 

Nature Communications. 2023. Vol. 14, num. Article number: 2875. DOI : 10.1038/s41467-023-38491-9.

Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain

L. Dumas; M. Marfoglia; B. Yang; M. Hijazi; A. Larabi et al. 

2023. DOI : 10.1101/2023.04.05.535724.

Conference Papers

Designed Tumor Microenvironment Responsive Biosensors Enhance Chimeric Antigen Receptor T Cell Therapy for Cancer

J. A. Rath; L. S. Powell-Rudden; N. Nouraee; P. Barth; C. Arber 

2023.  p. 79 – 79.

2022

Journal Articles

Computationally designed GPCR quaternary structures bias signaling pathway activation

J. S. Paradis; X. Feng; B. Murat; R. E. Jefferson; B. Sokrat et al. 

Nature Communications. 2022. Vol. 13, num. 1, p. 6826. DOI : 10.1038/s41467-022-34382-7.

Computational design of ultrasensitive flexible peptide:receptor signaling complexes for enhanced chemotaxis

R. Jefferson; A. Oggier; A. Fuglistaler; N. Camviel; M. Hijazi et al. 

bioRxiv. 2022. DOI : 10.1101/2022.03.30.486413.

Reviews

Deep learning approaches for conformational flexibility and switching properties in protein design

L. S. P. Rudden; M. Hijazi; P. Barth 

Frontiers in Molecular Biosciences. 2022. Vol. 9, p. 928534. DOI : 10.3389/fmolb.2022.928534.

Working Papers

Computational rewiring of allosteric pathways reprograms GPCR selective responses to ligands

D. Keri; M. Hijazi; A. Oggier; P. Barth 

2022

2021

Journal Articles

Computational design of highly signaling active membrane receptors through de novo solvent-mediated allosteric networks

-Y. Chen; J. Lai; J. Wang; A. Russell; K. Conners et al. 

bioRxiv. 2021. DOI : 10.1101/2021.09.29.462228.

Computationally-guided tuning of ligand sensitivity in a GPCR-based sensor

D. Keri; R. B. Cola; Z. Kagiampaki; P. Tommaso; P. Barth 

bioRxiv. 2021. DOI : 10.1101/2021.09.21.461282.

Computationally designed GPCR quaternary structures bias signaling pathway activation

J. S. Paradis; X. Feng; B. Murat; R. Jefferson; M. Szpakowska et al. 

bioRxiv. 2021. DOI : 10.1101/2021.09.23.461493.

Conference Papers

Computationally designed GPCR quaternary structures bias signaling pathway activation

R. Jefferson; X. Feng; P. Barth; J. Paradis; M. Bouvier et al. 

2021.  p. 51 – 51.

Theses

Reprogramming G Protein-Coupled Receptor Structure, Function And Signaling By Computational Design

D. Kéri / P. D. Barth (Dir.)  

Lausanne, EPFL, 2021. 

Patents

Method for generating variants of a protein

P. Barth 

US2023227534; EP4004925; WO2021018756; EP3772065.

2021.

Method for generating variants of a protein

P. Barth 

US2023227534; EP4004925; WO2021018756; EP3772065.

2021.

2020

Journal Articles

Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane

J. Yin; K-Y. M. Chen; M. J. Clark; M. Hijazi; P. Kumari et al. 

Nature. 2020. Vol. 584, num. 7819, p. 125 – 129. DOI : 10.1038/s41586-020-2379-5.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

J. K. Leman; B. D. Weitzner; S. M. Lewis; J. Adolf-Bryfogle; N. Alam et al. 

Nature Methods. 2020. Vol. 17, p. 665 – 680. DOI : 10.1038/s41592-020-0848-2.

An autism-linked missense mutation in SHANK3 reveals the modularity of Shank3 function

L. Wang; K. Pang; K. Han; C. J. Adamski; W. Wang et al. 

Molecular Psychiatry. 2020. Vol. 25, p. 2534 – 2555. DOI : 10.1038/s41380-018-0324-x.

Computational design of G Protein-Coupled Receptor allosteric signal transductions

K-Y. M. Chen; D. Keri; P. Barth 

Nature Chemical Biology. 2020. Vol. 16, p. 77 – 86. DOI : 10.1038/s41589-019-0407-2.

2018

Journal Articles

Reprogramming G protein coupled receptor structure and function

D. Keri; P. Barth 

Current Opinion in Structural Biology. 2018. Vol. 51, p. 187 – 194. DOI : 10.1016/j.sbi.2018.07.008.

Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways

M. Young; T. Dahoun; B. Sokrat; C. Arber; K. M. Chen et al. 

Proceedings of the National Academy of Sciences. 2018. Vol. 115, num. 27, p. 7051 – 7056. DOI : 10.1073/pnas.1718489115.

Conference Papers

Computational design of GPCR structure, stability and function

P. Barth 

2018. 255th National Meeting and Exposition of the American-Chemical-Society (ACS) – Nexus of Food, Energy, and Water, New Orleans, LA, Mar 18-22, 2018.

2017

Journal Articles

Reprogramming cellular functions with engineered membrane proteins

C. Arber; M. Young; P. Barth 

Current Opinion in Biotechnology. 2017. Vol. 47, p. 92 – 101. DOI : 10.1016/j.copbio.2017.06.009.

Computational design of ligand-binding membrane receptors with high selectivity

X. Feng; J. Ambia; K-Y. M. Chen; M. Young; P. Barth 

Nature Chemical Biology. 2017. Vol. 13, num. 7, p. 715 – 723. DOI : 10.1038/nchembio.2371.

Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions

J. K. Lai; J. Ambia; Y. Wang; P. Barth 

Structure. 2017. Vol. 25, num. 11, p. 1758 – 1770.e8. DOI : 10.1016/j.str.2017.09.002.

2016

Journal Articles

Introduction of a polar core into the de novo designed protein Top7

B. Basanta; K. K. Chan; P. Barth; T. King; T. R. Sosnick et al. 

Protein Science. 2016. Vol. 25, num. 7, p. 1299 – 1307. DOI : 10.1002/pro.2899.

Toward high-resolution computational design of the structure and function of helical membrane proteins

P. Barth; A. Senes 

Nature Structural & Molecular Biology. 2016. Vol. 23, num. 6, p. 475 – 480. DOI : 10.1038/nsmb.3231.

A topological and conformational stability alphabet for multipass membrane proteins

X. Feng; P. Barth 

Nature Chemical Biology. 2016. Vol. 12, num. 3, p. 167 – 173. DOI : 10.1038/nchembio.2001.

2015

Journal Articles

Evolutionary-guided de novo structure prediction of self-associated transmembrane helical proteins with near-atomic accuracy

Y. Wang; P. Barth 

Nature Communications. 2015. Vol. 6, num. 1, p. 7196. DOI : 10.1038/ncomms8196.

Survivin-specific T cell receptor targets tumor but not T cells

C. Arber; X. Feng; H. Abhyankar; E. Romero; M-F. Wu et al. 

Journal of Clinical Investigation. 2015. Vol. 125, num. 1, p. 157 – 168. DOI : 10.1172/JCI75876.

2014

Journal Articles

Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges

I. Kufareva; V. Katritch; R. Stevens; R. Abagyan 

Structure. 2014. Vol. 22, num. 8, p. 1120 – 1139. DOI : 10.1016/j.str.2014.06.012.