BMC Research NotesD. Chang, et al., "Prediction of protein secondary structures with a novel kernel density estimation based classifier," BMC Research Notes, vol. 1, p. 51, 2008. :Chang DTH, Ou YY, Hung HG, Yang
Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence1. This problem is of fundamental importance as the structure of a protein largely determines its function2; however, protein structures can be difficult to determine experimental...
like every other secondary structure prediction method, PSIPRED does not perform as well on single sequences. Any secondary structure prediction based on a single sequence should be considered as unreliable. Before running PSIPRED, please check the runpsipred and runpsipred_single scripts to see if ...
The prediction of protein structures has had a long and varied development, which is extensively covered in a number of reviews14,40,41,42,43. Despite the long history of applying neural networks to structure prediction14,42,43, they have only recently come to improve structure prediction10,11...
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on multiple sequence alignments (MSAs) as inputs to learn the co-evolution informa
specific properties (Schneider and Wrede1994Cui et al.2007), microarray data (Brown et al.2000) and protein secondary structure prediction (Ward et al.2003). Ong andet al.showed that currently used descriptors are generally useful for classifying proteins and the prediction performance may be ...
Jones D: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195–202. 10.1006/jmbi.1999.3091 Article CAS PubMed Google Scholar Thompson J, Higgins D, Gibson T: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment...
SidechainNet is a protein structure prediction dataset that directly extendsProteinNet2by Mohammed AlQuraishi. Specifically, SidechainNet adds measurements for protein angles and coordinates that describe the complete, all-atom protein structure (backboneandsidechain, excluding hydrogens) instead of the protei...
Proteins are composed of one or more chains of amino acids, and exhibit several levels of structure. The primary structure is defined by the sequence of amino acids comprising each chain, while the secondary structure is defined by local, repetitive spatial arrangements, which falls into three bas...
On the other hand, an additional benefit of introducing the FOD model into the current study is the possibility of identifying the source of failure in the 2LGN structure prediction process. It reveals a need to modify the external field, but also precisely defines the form of such modification...