Journal of chemical information and modeling
Mar 30, 2020
Despite significant advances in resolution, the potential for cryo-electron microscopy (EM) to be used in determining the structures of protein-drug complexes remains unrealized. Determination of accurate structures and coordination of bound ligands ...
The discovery of targeted drugs heavily relies on three-dimensional (3D) structures of target proteins. When the 3D structure of a protein target is unknown, it is very difficult to design its corresponding targeted drugs. Although the 3D structures ...
As an important category of proteins, alpha-helix transmembrane proteins (TMPs) play an important role in various biological activities. Because the solved αTMP structures are inadequate, predicting the residue contacts among the transmembrane segmen...
Journal of chemical information and modeling
Mar 11, 2020
Accurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Because of the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. ...
Cryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on a...
The intricate details of how proteins bind to proteins, DNA, and RNA are crucial for the understanding of almost all biological processes. Disease-causing sequence variants often affect binding residues. Here, we described a new, comprehensive system...
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...
Biochimica et biophysica acta. General subjects
Jan 16, 2020
Selecting peptides that bind strongly to the major histocompatibility complex (MHC) for inclusion in a vaccine has therapeutic potential for infections and tumors. Machine learning models trained on sequence data exist for peptide:MHC (p:MHC) binding...
Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence. This problem is of fundamental importance as the structure of a protein largely determines its function; however, protein str...
Detecting crossovers in cryo-electron microscopy images of protein fibrils is an important step towards determining the morphological composition of a sample. Currently, the crossover locations are picked by hand, which introduces errors and is a tim...