Intrinsically disordered proteins and multicellular organisms
Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry
out numerous biological functions, especially those associated with signaling, transcription …
out numerous biological functions, especially those associated with signaling, transcription …
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
In the field of artificial intelligence, a combination of scale in data and model capacity
enabled by unsupervised learning has led to major advances in representation learning and …
enabled by unsupervised learning has led to major advances in representation learning and …
Protein knots and fold complexity: some new twists
WR Taylor - Computational biology and chemistry, 2007 - Elsevier
The current knowledge on topological knots in protein structure is reviewed, considering in
turn, knots with three, four and five strand crossings. The latter is the most recent to be …
turn, knots with three, four and five strand crossings. The latter is the most recent to be …
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
ES Wright - BMC bioinformatics, 2015 - Springer
Background Alignment of large and diverse sequence sets is a common task in biological
investigations, yet there remains considerable room for improvement in alignment quality …
investigations, yet there remains considerable room for improvement in alignment quality …
Sixty-five years of the long march in protein secondary structure prediction: the final stretch?
Protein secondary structure prediction began in 1951 when Pauling and Corey predicted
helical and sheet conformations for protein polypeptide backbone even before the first …
helical and sheet conformations for protein polypeptide backbone even before the first …
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
Protein intrinsic disorder is becoming increasingly recognized in proteomics research. While
lacking structure, many regions of disorder have been associated with biological function …
lacking structure, many regions of disorder have been associated with biological function …
Analysis of molecular recognition features (MoRFs)
Several proteomic studies in the last decade revealed that many proteins are either
completely disordered or possess long structurally flexible regions. Many such regions were …
completely disordered or possess long structurally flexible regions. Many such regions were …
SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion …
Accurate prediction of protein secondary structure is essential for accurate sequence
alignment, three‐dimensional structure modeling, and function prediction. The accuracy of …
alignment, three‐dimensional structure modeling, and function prediction. The accuracy of …
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network
Because a nearly constant distance between two neighbouring Cα atoms, local backbone
structure of proteins can be represented accurately by the angle between Cαi− 1 Cαi …
structure of proteins can be represented accurately by the angle between Cαi− 1 Cαi …
Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training
An integrated system of neural networks, called SPINE, is established and optimized for
predicting structural properties of proteins. SPINE is applied to three‐state secondary …
predicting structural properties of proteins. SPINE is applied to three‐state secondary …