Coupled prediction of protein secondary and tertiary structure [PDF]
Proceedings of the National Academy of Sciences of the United States of America, 2003 The strong coupling between secondary and tertiary structure formation in protein folding is neglected in most structure prediction methods. In this work we investigate the extent to which nonlocal interactions in predicted tertiary structures can be used to improve secondary structure prediction.
Jens Meiler, David Baker, Meiler Jens
exaly +3 more sources
Recent Progress of Protein Tertiary Structure Prediction
MoleculesThe prediction of three-dimensional (3D) protein structure from amino acid sequences has stood as a significant challenge in computational and structural bioinformatics for decades.
Qiqige Wuyun +7 more
doaj +3 more sources
Molecular and in silico analysis of the coat protein of hibiscus chlorotic ringspot virus isolates [PDF]
Journal of Crop Protection, 2023 Hibiscus chlorotic ringspot virus (HCRSV), genus Betacarmovirus, family Tombusviridae, is a common pathogen of hibiscus plants in tropical and subtropical regions. During 2020-2021, leaf samples of Chinese hibiscus Hibiscus rosa-sinensis L. with mottling
Nadia Mosharaf +4 more
doaj +1 more source
Fast and accurate protein structure search with Foldseek
bioRxiv, 2022 Foldseek speeds up protein structural search by four to five orders of magnitude. As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck.
Michel van Kempen +7 more
semanticscholar +1 more source
Before and after AlphaFold2: An overview of protein structure prediction
Frontiers in Bioinformatics, 2023 Three-dimensional protein structure is directly correlated with its function and its determination is critical to understanding biological processes and addressing human health and life science problems in general.
L. Bertoline +3 more
semanticscholar +1 more source
Accurate protein structure prediction with hydroxyl radical protein footprinting data
Nature Communications, 2021 Hydroxyl radical protein footprinting (HRPF) in combination with mass spectrometry reveals the relative solvent exposure of labeled residues within a protein, thereby providing insight into protein tertiary structure.
S. Biehn, Steffen Lindert
semanticscholar +1 more source
Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15
Communications Chemistry, 2023 Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction.
Jian Liu +5 more
doaj +1 more source
Image-based effective feature generation for protein structural class and ligand binding prediction [PDF]
PeerJ Computer Science, 2020 Proteins are the building blocks of all cells in both human and all living creatures of the world. Most of the work in the living organism is performed by proteins.
Nafees Sadique +4 more
doaj +2 more sources
I 3D3P: an Intelligent 3D Protein Prediction Platform
Proceedings of the International Conference on Applied Innovations in IT, 2022 Proteins are macromolecules consisting of a chain of smaller molecules (i.e. amino acids) known as monomers. Three levels of protein structure are distinguished: primary, secondary and tertiary.
Mohamed Hachem Kermani, Zizette Boufaida
doaj +1 more source
Improved protein structure prediction by deep learning irrespective of co-evolution information
Nature Machine Intelligence, 2020 Predicting the tertiary structure of a protein from its primary sequence has been greatly improved by integrating deep learning and co-evolutionary analysis, as shown in CASP13 and CASP14. We describe our latest study of this idea, analysing the efficacy
Jinbo Xu, Matthew McPartlon, Jin Li
semanticscholar +1 more source