Before and after AlphaFold2: An overview of protein structure prediction
Three-dimensional protein structure is directly correlated with its function and its
determination is critical to understanding biological processes and addressing human …
determination is critical to understanding biological processes and addressing human …
Protein structure prediction: conventional and deep learning perspectives
Protein structure prediction is a way to bridge the sequence-structure gap, one of the main
challenges in computational biology and chemistry. Predicting any protein's accurate …
challenges in computational biology and chemistry. Predicting any protein's accurate …
JPred4: a protein secondary structure prediction server
Abstract JPred4 (http://www. compbio. dundee. ac. uk/jpred4) is the latest version of the
popular JPred protein secondary structure prediction server which provides predictions by …
popular JPred protein secondary structure prediction server which provides predictions by …
Protein secondary structure prediction based on position-specific scoring matrices
A two-stage neural network has been used to predict protein secondary structure based on
the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and …
the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and …
Twilight zone of protein sequence alignments
Sequence alignments unambiguously distinguish between protein pairs of similar and non-
similar structure when the pairwise sequence identity is high (> 40% for long alignments) …
similar structure when the pairwise sequence identity is high (> 40% for long alignments) …
The predictprotein server
Abstract PredictProtein (http://www. predictprotein. org) is an Internet service for sequence
analysis and the prediction of protein structure and function. Users submit protein …
analysis and the prediction of protein structure and function. Users submit protein …
Advances in homology protein structure modeling
Z **ang - Current Protein and Peptide Science, 2006 - benthamdirect.com
Homology modeling plays a central role in determining protein structure in the structural
genomics project. The importance of homology modeling has been steadily increasing …
genomics project. The importance of homology modeling has been steadily increasing …
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
A new dataset of 396 protein domains is developed and used to evaluate the performance of
the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR …
the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR …
The HD domain defines a new superfamily of metal-dependent phosphohydrolases
Nucleic acid polymerases and helicases often contain additional domains that possess
nuclease or phosphohydrolase activity; these domains also tend to occur as 'stand …
nuclease or phosphohydrolase activity; these domains also tend to occur as 'stand …
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties …
Motivation: In recent years, development of a single-method fold-recognition server lags
behind consensus and multiple template techniques. However, a good consensus …
behind consensus and multiple template techniques. However, a good consensus …