Parisa Hosseinzadeh

Binding of a Macrocyclic Nonapeptide Inhibitor to Histone Deacetylase 6

The paper reports the crystal structure of HDAC6 CD2 complexed with a macrocyclic nonapeptide inhibitor, revealing key interactions that contribute to its inhibitory potency.

From Code to Cure: Computationally Designed BMP-2 Binders Using AI-Integrated Pipelines for Controlled Bone Regeneration

This paper designs BMP-2 binders using AI pipelines to control bone regeneration, finding a binder with 2.07 nM affinity for BMP-2.

CyclicMPNN: Stable Cyclic Peptide Sequence Generation

The paper introduces CyclicMPNN, a model that generates energetically stable cyclic peptide sequences by fine-tuning ProteinMPNN with structural and in silico data, improving success rates in folding into generated backbones.

Applying computational protein design to engineer affibodies for affinity-controlled delivery of vascular endothelial growth factor and platelet-derived growth factor

This paper engineers affibodies with tunable affinities for VEGF and PDGF using computational design and yeast display to improve controlled protein release from hydrogels.

De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors

This paper presents computational methods for designing GPCR-binding miniproteins and validates them through high-throughput screening, producing agonists and antagonists for multiple GPCRs.

CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Conformational Sampling

CyclicCAE generates energetically favorable macrocycle conformations faster than Rosetta's GeneralizedKIC, using synthetic data and enabling design and structure prediction.

The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design

The paper introduces Masala, an open-source software suite designed to extend and improve upon Rosetta for synthetic heteropolymer design, offering modular architecture and performance improvements.