A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
Domain enhanced lookup time accelerated BLAST
GM Boratyn, AA Schäffer, R Agarwala, SF Altschul… - Biology direct, 2012 - Springer
Background BLAST is a commonly-used software package for comparing a query sequence
to a database of known sequences; in this study, we focus on protein sequences. Position …
to a database of known sequences; in this study, we focus on protein sequences. Position …
Automated structure-and sequence-based design of proteins for high bacterial expression and stability
Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in
low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic …
low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic …
Sequence similarity searching
Sequence similarity searching has become an important part of the daily routine of
molecular biologists, bioinformaticians and biophysicists. With the rapidly growing sequence …
molecular biologists, bioinformaticians and biophysicists. With the rapidly growing sequence …
Computational design of stable and soluble biocatalysts
M Musil, H Konegger, J Hon, D Bednar… - Acs Catalysis, 2018 - ACS Publications
Natural enzymes are delicate biomolecules possessing only marginal thermodynamic
stability. Poorly stable, misfolded, and aggregated proteins lead to huge economic losses in …
stability. Poorly stable, misfolded, and aggregated proteins lead to huge economic losses in …
Prediction of 8-state protein secondary structures by a novel deep learning architecture
B Zhang, J Li, Q Lü - BMC bioinformatics, 2018 - Springer
Background Protein secondary structure can be regarded as an information bridge that links
the primary sequence and tertiary structure. Accurate 8-state secondary structure prediction …
the primary sequence and tertiary structure. Accurate 8-state secondary structure prediction …
Prediction of protein-protein interaction sites through eXtreme gradient boosting with kernel principal component analysis
X Wang, Y Zhang, B Yu, A Salhi, R Chen… - Computers in biology …, 2021 - Elsevier
Predicting protein-protein interaction sites (PPI sites) can provide important clues for
understanding biological activity. Using machine learning to predict PPI sites can mitigate …
understanding biological activity. Using machine learning to predict PPI sites can mitigate …
Sequence-based prediction of protein-protein interaction sites by simplified long short-term memory network
Proteins often interact with each other and form protein complexes to carry out various
biochemical activities. Knowledge of the interaction sites is helpful for understanding …
biochemical activities. Knowledge of the interaction sites is helpful for understanding …
Designed active-site library reveals thousands of functional GFP variants
Mutations in a protein active site can lead to dramatic and useful changes in protein activity.
The active site, however, is sensitive to mutations due to a high density of molecular …
The active site, however, is sensitive to mutations due to a high density of molecular …
Bacterial communities in a bioelectrochemical denitrification system: the effects of supplemental electron acceptors
Electrochemical treatment of nitrate (NO 3−), nitrite (NO 2−) and mixtures of nitrate and nitrite
was evaluated with microbial catalysts on a cathode in three different bioelectrochemical …
was evaluated with microbial catalysts on a cathode in three different bioelectrochemical …