Journal of chemical information and modeling
36533639
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabe...
Methods in molecular biology (Clifton, N.J.)
36959440
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The thres...
Allostery in proteins involves, broadly speaking, ligand-induced conformational transitions that modulate function at active sites distal to where the ligand binds. In contrast, the concept of cooperativity (in the sense used in phase transition theo...
[Formula: see text] With advances in imaging technologies and the development of artificial intelligence-based predictive software, has the protein folding problem finally been solved?
Proceedings of the National Academy of Sciences of the United States of America
37253017
Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to ...
Topologically knotted proteins have entangled structural elements within their native structures that cannot be disentangled simply by pulling from the N- and C-termini. Systematic surveys have identified different types of knotted protein structures...
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover nearly all proteins that are known, including thos...
BACKGROUND: The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the computational prediction of prote...