International journal of biological macromolecules
Aug 24, 2023
Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds pro...
INTRODUCTION: Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery...
Biochimica et biophysica acta. Proteins and proteomics
Aug 11, 2023
Over the last 40 years nuclear magnetic resonance (NMR) spectroscopy has established itself as one of the most versatile techniques for the characterization of biomolecules, especially proteins. Given the molecular size limitations of NMR together wi...
Biochimica et biophysica acta. Proteins and proteomics
Aug 9, 2023
Protein-protein interactions (PPIs) play a critical role in various biological processes. Accurately estimating the binding affinity of PPIs is essential for understanding the underlying molecular recognition mechanisms. In this study, we employed a ...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 9, 2023
Biomedical Named Entity Recognition (BioNER) aims at identifying biomedical entities such as genes, proteins, diseases, and chemical compounds in the given textual data. However, due to the issues of ethics, privacy, and high specialization of biomed...
Journal of chemical information and modeling
Aug 8, 2023
The present contribution introduces a novel computational protocol called PyRMD2Dock, which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular docking software AutoDock-GPU (AD4-GPU) to enhance the throughput of virtual sc...
This article reports and analyzes the results of protein complex model accuracy estimation by our methods (DeepUMQA3 and GraphGPSM) in the 15th Critical Assessment of techniques for protein Structure Prediction (CASP15). The new deep learning-based m...
Journal of the American Society for Mass Spectrometry
Aug 7, 2023
An original approach that adopts machine learning inference to predict protein structural information using hydrogen-deuterium exchange mass spectrometry (HDX-MS) is described. The method exploits an in-house optimization program that increases the r...
The human predictor team PEZYFoldings got first place with the assessor's formulae (3rd place with Global Distance Test Total Score [GDT-TS]) in the single-domain category and 10th place in the multimer category in Critical Assessment of Structure Pr...
We present VoroIF-GNN (Voronoi InterFace Graph Neural Network), a novel method for assessing inter-subunit interfaces in a structural model of a protein-protein complex, relying solely on the input structure without any additional information. Given ...
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