Journal of chemical information and modeling
Apr 8, 2015
Molecular docking, despite its undeniable usefulness in computer-aided drug design protocols and the increasing sophistication of tools used in the prediction of ligand-protein interaction energies, is still connected with a problem of effective resu...
OBJECTIVE: The objective of this paper is to highlight the state-of-the-art machine learning (ML) techniques in computational docking. The use of smart computational methods in the life cycle of drug design is relatively a recent development that has...
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
Accurate prediction of protein-peptide complex structures plays a critical role in structure-based drug design, including antibody design. Most peptide-docking benchmark studies were conducted using crystal structures of protein-peptide complexes; as...
Journal of chemical information and modeling
May 26, 2025
Machine learning algorithms have played a fundamental role in the development of therapeutic antibodies by being trained on data sets of sequences and/or structures. However, structural data sets remain limited, especially those that include antibody...
Journal of chemical information and modeling
May 26, 2025
Physics-based docking methods have long been the cornerstone of structure-based virtual screening (VS). However, the emergence of machine learning (ML)-based docking approaches has opened new possibilities for enhancing VS technologies. In this study...
Protein science : a publication of the Protein Society
May 1, 2025
Deep learning methods have played an increasingly pivotal role in advancing side-chain packing and mutation effect prediction (ΔΔG) for protein complexes. Although these two tasks are inherently closely related, they are typically treated separately ...
Protein structural fluctuations, measured by Debye-Waller factors or B-factors, are known to be closely associated with protein flexibility and function. Theoretical approaches have also been developed to predict B-factor values, which reflect protei...
Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient and effective quality assessment ...
Protein science : a publication of the Protein Society
Feb 1, 2025
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression...