D. del Alamo

Conformational sampling and interpolation using language-based protein folding neural networks

This paper shows that ESMFold can predict alternate protein conformations and generate interconversion paths between them using sequence embeddings from ESM2.

Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter

This paper investigates the conformational dynamics of the pH-dependent APC antiporter GadC using DEER spectroscopy and AlphaFold2 models, revealing acid-induced structural changes and substrate-specific dynamics.

Modeling of protein conformational changes with Rosetta guided by limited experimental data

This paper introduces ConfChangeMover (CCM), a Rosetta tool for modeling protein conformational changes using sparse experimental data, and shows it outperforms existing methods.

Sampling the conformational landscapes of transporters and receptors with AlphaFold2

This study uses AlphaFold2 to generate multiple conformations of transporters and GPCRs, showing that reducing MSA depth improves conformational sampling accuracy.

Protein fold prediction using simulated DEER distance distributions and decay traces

This paper introduces RosettaDEER, a method that simulates DEER distance distributions and decay traces to improve protein fold prediction using sparse experimental data.

Talent Identification at the limits of Peer Review: an analysis of the EMBO Postdoctoral Fellowships Selection Process

The paper evaluates the EMBO Postdoctoral Fellowship selection process, finding peer review ineffective beyond initial pre-selection and proposing a mixed model with random allocation for final awards.