The journal of physical chemistry letters
Aug 2, 2024
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously...
International journal of molecular sciences
Aug 1, 2024
Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established pr...
European journal of medicinal chemistry
Jul 31, 2024
The molecular generation models based on protein structures represent a cutting-edge research direction in artificial intelligence-assisted drug discovery. This article aims to comprehensively summarize the research methods and developments by analyz...
Protein design and engineering are evolving at an unprecedented pace leveraging the advances in deep learning. Current models nonetheless cannot natively consider non-protein entities within the design process. Here, we introduce a deep learning appr...
Journal of computer-aided molecular design
Jul 17, 2024
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and an...
In recent years, there has been a notable increase in the scientific community's interest in rational protein design. The prospect of designing an amino acid sequence that can reliably fold into a desired three-dimensional structure and exhibit the i...
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and...
Acta crystallographica. Section D, Structural biology
Jun 27, 2024
When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification...
AlphaFold2 is an Artificial Intelligence-based program developed to predict the 3D structure of proteins given only their amino acid sequence at atomic resolution. Due to the accuracy and efficiency at which AlphaFold2 can generate 3D structure predi...
Journal of chemical information and modeling
Jun 26, 2024
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have eme...
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