Eva Rajh
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Eva Rajh has a total of 16 co-authors. Here are the top co-authors by number of shared publications:
- Ajasja Ljubetič
Department of Synthetic Biology and Immunology, Ljubljana, National Institute of Chemistry, 1000 Ljubljana, Slovenia
2 shared publications - Federico Olivieri
Department of Synthetic Biology and Immunology, Ljubljana, National Institute of Chemistry, 1000 Ljubljana, Slovenia
2 shared publications - Alina V. Konstantinova
Department of Synthetic Biology and Immunology, Ljubljana, National Institute of Chemistry, 1000 Ljubljana, Slovenia
1 shared publication - David Baker
Department of Biochemistry, University of Washington, Seattle, WA, USA
1 shared publication - Eric M. Lynch
Department of Biochemistry, University of Washington, Seattle, USA
1 shared publication - Hao Shen
Institute for Protein Design, University of Washington, Seattle, US
1 shared publication
Latest Publications
- Open Access
Prosculpt: Lowering the Barrier to Computational Protein Design
Over the past decade, protein design has evolved from a specialized discipline into a broadly accessible approach for engineering and interrogating biological systems. Despite these advances, protein design continues to be a technically challenging task, often requiring knowledge of programming to be able to use and combine the different software packages. To address this challenge, we have developed Prosculpt, an easy-to-use protein design pipeline. Prosculpt integrates RFdiffusion for backbone generation, ProteinMPNN for sequence design and multiple structure-prediction platforms (AF2, AF3, Colabfold, Boltz2). Candidate designs are evaluated using customizable Rosetta-based scoring protocols. Each project is specified through a single configuration file, enabling users with minimal computational expertise to perform sophisticated protein design tasks without writing code, while also allowing advanced users to access the full capabilities of the underlying programs. Prosculpt supports a wide range of applications, including design of symmetric homo-oligomers, design of binders, motif scaffolding, partial diffusion and fixed-backbone sequence redesign. By combining these capabilities within a single, user-friendly platform, Prosculpt provides a practical entry point to modern protein design for both novice and expert users.
Open AccessProsculpt: Lowering the Barrier to Computational Protein Design
Over the past decade, protein design has evolved from a specialized discipline into a broadly accessible approach for engineering and interrogating biological systems. Despite these advances, protein design continues to be a technically challenging task, often requiring knowledge of programming to be able to use and combine the different software packages. To address this challenge, we have developed Prosculpt, an easy-to-use protein design pipeline. Prosculpt integrates RFdiffusion for backbone generation, ProteinMPNN for sequence design and multiple structure-prediction platforms (AF2, AF3, Colabfold, Boltz2). Candidate designs are evaluated using customizable Rosetta-based scoring protocols. Each project is specified through a single configuration file, enabling users with minimal computational expertise to perform sophisticated protein design tasks without writing code, while also allowing advanced users to access the full capabilities of the underlying programs. Prosculpt supports a wide range of applications, including design of symmetric homo-oligomers, design of binders, motif scaffolding, partial diffusion and fixed-backbone sequence redesign. By combining these capabilities within a single, user-friendly platform, Prosculpt provides a practical entry point to modern protein design for both novice and expert users.
- Open Access
De-novo design of a random protein walker
Molecular machines hold great potential. Design of static monomeric and oligomeric protein structures has advanced tremendously, but few dynamic protein systems have been designed. Here we present the design and characterization of a random protein walker that diffuses along a designed protein track. For the track, we designed micro-meter long fibres and developed a method to rigidly decorate them with arbitrary proteins. The walkers consist of homo-oligomers that reversibly bind the track using heterodimeric feet; we tested multiple heterodimer interfaces for reversibility and designed six walkers with different numbers of feet. Cryo-EM experiments confirmed the structure of the track and walkers. We performed detailed single molecule tracking and kinetics characterisation and found that the walkers with more feet diffuse along the track faster. The system represents a tuneable starting point for future powered protein molecular robots.
Open AccessDe-novo design of a random protein walker
Molecular machines hold great potential. Design of static monomeric and oligomeric protein structures has advanced tremendously, but few dynamic protein systems have been designed. Here we present the design and characterization of a random protein walker that diffuses along a designed protein track. For the track, we designed micro-meter long fibres and developed a method to rigidly decorate them with arbitrary proteins. The walkers consist of homo-oligomers that reversibly bind the track using heterodimeric feet; we tested multiple heterodimer interfaces for reversibility and designed six walkers with different numbers of feet. Cryo-EM experiments confirmed the structure of the track and walkers. We performed detailed single molecule tracking and kinetics characterisation and found that the walkers with more feet diffuse along the track faster. The system represents a tuneable starting point for future powered protein molecular robots.