The core of large-scale drug virtual screening is to select the binders accurately and efficiently with high affinity from large libraries of small molecules in which non-binders are usually dominant. The binding affinity is significantly influenced ...
Proceedings of the National Academy of Sciences of the United States of America
May 30, 2023
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 ...
Building accurate protein models into moderate resolution (3-5 Å) cryoelectron microscopy (cryo-EM) maps is challenging and error prone. We have developed MEDIC (Model Error Detection in Cryo-EM), a robust statistical model that identifies local back...
Multiple sequence alignments (MSAs) are the workhorse of molecular evolution and structural biology research. From MSAs, the amino acids that are tolerated at each site during protein evolution can be inferred. However, little is known regarding the ...
Journal of chemical information and modeling
May 11, 2023
The accurate prediction of protein structures achieved by deep learning (DL) methods is a significant milestone and has deeply impacted structural biology. Shortly after its release, AlphaFold2 has been evaluated for predicting protein-peptide intera...
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six hypervariable loops that are diversified through genetic rec...
Proceedings of the National Academy of Sciences of the United States of America
Apr 24, 2023
With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics is encoded by the primary protein sequence so as to better predict ...
International journal of molecular sciences
Apr 7, 2023
Intrinsically disordered proteins (IDPs) account for more than 50% of the human proteome and are closely associated with tumors, cardiovascular diseases, and neurodegeneration, which have no fixed three-dimensional structure under physiological condi...
Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in differen...
The remarkable recent advances in protein structure prediction have enabled computational modeling of protein structures with considerably higher accuracy than ever before. While state-of-the-art structure prediction methods provide self-assessment c...