Acta crystallographica. Section D, Structural biology
Feb 27, 2023
Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold. Here, an automatic procedure requiring only sequence information and crystallographic data is presented th...
Protein Structure Prediction (PSP) has achieved significant progress lately. Prediction of inter-residue distances by machine learning and their exploitation during the conformational search is largely among the critical factors behind the progress. ...
In recent years, thanks to advances in computer hardware and dataset availability, data-driven approaches (like machine learning) have become one of the essential parts of the drug design framework to accelerate drug discovery procedures. Constructin...
Current sequence-based predictors of protein-binding residues (PBRs) belong to two distinct categories: structure-trained vs. intrinsic disorder-trained. Since disordered PBRs differ from structured PBRs in several ways, including ability to bind mul...
Acta crystallographica. Section D, Structural biology
Nov 25, 2022
Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the proce...
Despite the immense progress recently witnessed in protein structure prediction, the modeling accuracy for proteins that lack sequence and/or structure homologs remains to be improved. We developed an open-source program, DeepFold, which integrates s...
Three-dimensional protein structure prediction is one of the major challenges in bioinformatics. According to recent research findings, real-valued distance prediction plays a vital role in determining the unique three-dimensional protein structure. ...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 8, 2022
DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) are two important nucleic acid-binding proteins (NABPs), which play important roles in biological processes such as replication, translation and transcription of genetic material. Some prote...
Most proteins in cells are composed of multiple folding units (or domains) to perform complex functions in a cooperative manner. Relative to the rapid progress in single-domain structure prediction, there are few effective tools available for multi-d...
International journal of molecular sciences
Jul 12, 2022
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids)....