Pacesa Lab
Biomolecular design • De novo Biology • AI Therapy

Pacesa lab publications

2026

Target DNA binding-induced dimerization is required for long-A prokaryotic Argonaute-mediated immunity
Barendse P, van Drimmelen M, Pacesa M, Sivamaran A, Zhang D-K, Nickel L, Niault T, Lindhoud S, Roosjen M, Hegge J, Park KL, Correia BC, van der Oost J, Joo C, Westphal A, Swarts DC
Preprint
BindCraft
Argonaute
Protein binder
4 May 2026
Target DNA binding-induced dimerization is required for long-A prokaryotic Argonaute-mediated immunity
Deep Learning-based Design of Peptide Binders
Pacesa M
Chimia
Review
Peptide Design
29 April 2026
Deep Learning-based Design of Peptide Binders
Inference-time optimization for experiment-grounded protein ensemble generation
Maddipatla A, Rzayev A, Pegoraro M, Marx A, Pacesa M, Schanda P, Vedula S, Bronstein AM
arXiv
ML
Structure Prediction
CryoEM
X-tal
NMR
4 March 2026
Inference-time optimization for experiment-grounded protein ensemble generation

2025

One-shot design of functional protein binders with BindCraft
Pacesa M*, Nickel L*, Schellhaas C*, Schmidt J, Pyatova K, Kissling L, Barendse P, Choudhury J, Kapoor S, Alcaraz-Serna A, Cho Y, Ghamary KH, Vinue L, Yachnin BJ, Wollacott AM, Buckley S, Westphal AH, Lindhoud S, Georgeon S, Goverde CA, Hatzopoulos GN, Gonczy P, Muller YD, Schwank G, Swarts DC, Vecchio AJ, Schneider BL, Ovchinnikov S, Correia BE
Nature
BindCraft
ML
Pipeline
Protein binder
AAV
27 August 2025
One-shot design of functional protein binders with BindCraft
Design of highly functional genome editors by modelling CRISPR–Cas sequences
Ruffolo JA*, Nayfach S*, Gallagher J*, Bhatnagar A*, Beazer J, Hussain R, Russ J, Yip J, Hill E, Pacesa M, Meeske AJ, Cameron P, Madani A
Nature
ML
Enzyme design
CRISPR-Cas
Genome Editing
30 July 2025
Design of highly functional genome editors by modelling CRISPR–Cas sequences
Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition
Cotet T-S, Krawczuk I, Stocco F, Ferruz N, Gitter A, Kurumida Y, Machado LA, Paesani F, Calia CN, Challacombe CA, Haas N, Qamar A, Correia BE, Pacesa M, Nickel L, Subr K, Castorina LV, Campbell MJ, Ferragu C, Kidger P, Hallee L, Wood CW, Stam MJ, Klounis T, Unal SM, Belot E, Naka A, Adaptyv Competition Organizers
bioRxiv
BindCraft
Competition
Protein binder
24 April 2025
Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition
Boltzdesign1: Inverting all-atom structure prediction model for generalized biomolecular binder design
Cho Y, Pacesa M, Zhang Z, Correia BE, Ovchinnikov S
bioRxiv
ML
Pipeline
Protein binder
Ligand binder
6 April 2025
Boltzdesign1: Inverting all-atom structure prediction model for generalized biomolecular binder design

2024

Computational design of soluble and functional membrane protein analogues
Goverde CA*, Pacesa M*, Goldbach N*, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE
Nature
SolubleMPNN
ML
Pipeline
Membrane protein solubilisation
Fold design
Scaffolding
19 June 2024
Computational design of soluble and functional membrane protein analogues
Past, present, and future of CRISPR genome editing technologies
Pacesa M*, Pelea O*, Jinek M
Cell
Review
CRISPR-Cas
Gene editing
29 February 2024
Past, present, and future of CRISPR genome editing technologies
An atlas of protein homo-oligomerization across domains of life
Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED
Cell
ML
Structure Prediction
Protein assemblies
15 February 2024
An atlas of protein homo-oligomerization across domains of life

2022

Structural basis of SpCas9 off-target tolerance
Pacesa M, Lin C-H, Clery A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FHT, Palermo G, Cameron P, Donohoue PD, Jinek M:
Cell
CRISPR-Cas
X-tal
Nucleic acid
27 October 2022
Structural basis of SpCas9 off-target tolerance
Mechanism of R-loop formation and conformational activation of Cas
Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M
Nature
CRISPR-Cas
CryoEM
Nucleic acid
24 August 2022
Mechanism of R-loop formation and conformational activation of Cas

2021

Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells
Donohoue P*, Pacesa M*, Lau E, Vidal BM, Irby MJ, Nyer DB, Rotstein T, Banh L, Toh MS, Kohrs B, Baek K, Slorach EM, van Overbeek M, Fuller CK, May AP, Jinek M, Cameron P
Molecular Cell
CRISPR-Cas
X-tal
Gene editing
Nucleic acid
2 September 2021
Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells