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Abstract AlphaFold2 has revolutionized protein structure prediction from amino‐acid sequence. In addition to protein structures, high‐resolution dynamics information about various protein regions is important for understanding protein function. Although AlphaFold2 has neither been designed nor trained to predict protein dynamics, it is shown here how the information returned by AlphaFold2 can be used to predict dynamic protein regions at the individual residue level. The approach, which is termed cdsAF2, uses the 3D protein structure returned by AlphaFold2 to predict backbone NMR NHS2order parameters using a local contact model that takes into account the contacts made by each peptide plane along the backbone with its environment. By combining for each residue AlphaFold2's pLDDT confidence score for the structure prediction accuracy with the predictedS2value using the local contact model, an estimator is obtained that semi‐quantitatively captures many of the dynamics features observed in experimental backbone NMR NHS2order parameter profiles. The method is demonstrated for a set nine proteins of different sizes and variable amounts of dynamics and disorder.
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DIPS-Plus: The enhanced database of interacting protein structures for interface prediction
Abstract In this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for machine learning of protein interfaces. While the original DIPS dataset contains only the Cartesian coordinates for atoms contained in the protein complex along with their types, DIPS-Plus contains multiple residue-level features including surface proximities, half-sphere amino acid compositions, and new profile hidden Markov model (HMM)-based sequence features for each amino acid, providing researchers a curated feature bank for training protein interface prediction methods. We demonstrate through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.
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- PAR ID:
- 10438391
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Data
- Volume:
- 10
- Issue:
- 1
- ISSN:
- 2052-4463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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