What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds. J Durairaj, AM Waterhouse, T Mets, T Brodiazhenko, M Abdullah,...

2023年6月13日 · It performs fragment-linking using reinforcement learning on an autoregressive SMILES generator. The method optimizes for a composite score combining relevant physicochemical properties and a novel, attention-based point cloud alignment score.

2022年11月7日 · Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling...

2023年1月1日 · To facilitate this, we 1) document recent advances in deep learning (DL) assisted protein design from the last three years, 2) present a practical pipeline that allows to go from de novo-generated sequences to their predicted properties and web-powered visualization within minutes, and 3) leverage it to suggest a generated protein sequence which...

Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data.

Mehmet AKDEL, PhD Student | Cited by 278 | of Wageningen University & Research, Wageningen (WUR) | Read 15 publications | Contact Mehmet AKDEL

2023年2月16日 · Akdel et al. 4 assess AlphaFold2 across multiple tasks, including its structural coverage of multiple proteomes, the extent of fold space it models and its ability to predict ligand...

2023年9月13日 · By exploring this network, we discovered 290 putative new protein families, identified at least one new protein fold and defined a new superfamily of translation-targeting toxin–antitoxin (TA)...

2021年9月26日 · Here, we evaluate the use of AlphaFold 2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modelling of interactions; and modelling of experimental structural data.

A software-suite to perform multiple protein structure alignment and structure feature extraction. A structure-based, alignment-free embedding approach for proteins. Can be used as input to …