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. 


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. 2023-05-19. 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. 

2023-04-06. 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 

2023-05-01.  p. 79-79.


Variants of the gain domain of adhesion g protein-coupled receptors

M. Marfoglia; L. Dumas; P. Barth 



Designed biosensors for enhanced t cell therapy

C. Arber; P. Barth; J. A. Rath; L. Rudden 



Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis

P. Barth; R. Jefferson 




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. 2022-11-11. 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. 2022-04-01. DOI : 10.1101/2022.03.30.486413.


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

L. S. P. Rudden; M. Hijazi; P. Barth 

Frontiers in Molecular Biosciences. 2022-08-10. 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 



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. 2021-10-01. 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. 2021-09-24. 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. 2021-09-23. 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. 

2021-10-01.  p. 51-51.


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

D. Kéri / P. D. Barth (Dir.)  

Lausanne, EPFL, 2021. 


Method for generating variants of a protein

P. Barth 

US2023227534; EP4004925; WO2021018756; EP3772065.


Method for generating variants of a protein

P. Barth 

US2023227534; EP4004925; WO2021018756; EP3772065.



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. 2020-08-06. 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. 2020-06-01. Vol. 17, p. 665–680. DOI : 10.1038/s41592-020-0848-2.

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.

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.


Journal Articles

Reprogramming G protein coupled receptor structure and function

D. Keri; P. Barth 

Current Opinion in Structural Biology. 2018-07-25. Vol. 51, p. 187-194. DOI : 10.1016/

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. 2018-07-13. Vol. 115, num. 27, p. 7051-7056. DOI : 10.1073/pnas.1718489115.

Conference Papers

Computational design of GPCR structure, stability and function

P. Barth 

2018-03-18. 255th National Meeting and Exposition of the American-Chemical-Society (ACS) – Nexus of Food, Energy, and Water, New Orleans, LA, Mar 18-22, 2018.


Journal Articles

Reprogramming cellular functions with engineered membrane proteins

C. Arber; M. Young; P. Barth 

Current Opinion in Biotechnology. 2017-10-01. 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. 2017-07-13. 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.


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. 2016-07-26. 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. 2016-06-07. 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. 2016-03-12. Vol. 12, num. 3, p. 167-173. DOI : 10.1038/nchembio.2001.


Journal Articles

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

Y. Wang; P. Barth 

Nature Communications. 2015-05-21. 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. 2015-01-01. Vol. 125, num. 1, p. 157-168. DOI : 10.1172/JCI75876.


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. 2014-08-05. Vol. 22, num. 8, p. 1120-1139. DOI : 10.1016/j.str.2014.06.012.

High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues

A. Schlessinger; K-Y. M. Chen; J. Sun; J. S. Salvo; D. Baker et al. 

PLoS Computational Biology. 2014-05-22. Vol. 10, num. 5, p. e1003636. DOI : 10.1371/journal.pcbi.1003636.


Journal Articles

Novel Conserved Genotypes Correspond to Antibiotic Resistance Phenotypes of E. coli Clinical Isolates

W. van Schaik; M. C. Swick; M. A. Evangelista; T. J. Bodine; J. R. Easton-Marks et al. 

PLoS ONE. 2013-06-18. Vol. 8, num. 6, p. e65961. DOI : 10.1371/journal.pone.0065961.


Journal Articles

Naturally evolved G protein-coupled receptors adopt metastable conformations

K-Y. M. Chen; F. Zhou; B. G. Fryszczyn; P. Barth 

Proceedings of the National Academy of Sciences. 2012-08-04. Vol. 109, num. 33, p. 13284-13289. DOI : 10.1073/pnas.1205512109.


Journal Articles

Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment

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

Structure. 2011-08-10. Vol. 19, num. 8, p. 1108-1126. DOI : 10.1016/j.str.2011.05.012.


Journal Articles

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

M. Michino; E. Abola; C. L. Brooks; J. S. Dixon; J. Moult et al. 

Nature Reviews Drug Discovery. 2009-06-08. Vol. 8, num. 6, p. 455-463. DOI : 10.1038/nrd2877.

The Structure of a Receptor with Two Associating Transmembrane Domains on the Cell Surface: Integrin αIIbβ3

J. Zhu; B-H. Luo; P. Barth; J. Schonbrun; D. Baker et al. 

Molecular Cell. 2009-04-24. Vol. 34, num. 2, p. 234-249. DOI : 10.1016/j.molcel.2009.02.022.