A5011129866- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Multimodal Machine Learning Applications
- Protein Structure and Dynamics
- Natural Language Processing Techniques
- Topic Modeling
- Signaling Pathways in Disease
OpenBiome
2024
University of Parma
2021-2023
Cape Eleuthera Institute
2022
Abstract AlphaFold2 revolutionized structural biology with the ability to predict protein structures exceptionally high accuracy. Its implementation, however, lacks code and data required train new models. These are necessary (i) tackle tasks, like protein-ligand complex structure prediction, (ii) investigate process by which model learns, remains poorly understood, (iii) assess model’s generalization capacity unseen regions of fold space. Here we report OpenFold, a fast, memory-efficient,...
AlphaFold2 revolutionized structural biology with the ability to predict protein structures exceptionally high accuracy. Its implementation, however, lacks code and data required train new models. These are necessary (1) tackle tasks, like protein–ligand complex structure prediction, (2) investigate process by which model learns (3) assess model's capacity generalize unseen regions of fold space. Here we report OpenFold, a fast, memory efficient trainable implementation AlphaFold2. We...
A bstract Self-supervised pretraining on protein sequences has led to state-of-the art performance function and fitness prediction. However, sequence-only methods ignore the rich information contained in experimental predicted structures. Meanwhile, inverse folding reconstruct a protein’s amino-acid sequence given its structure, but do not take advantage of that have known In this study, we train masked language model parameterized as structured graph neural network. During pretraining,...