MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
Motivation: Recent developments of statistical techniques to infer direct evolutionary
couplings between residue pairs have rendered covariation-based contact prediction a …
couplings between residue pairs have rendered covariation-based contact prediction a …
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
DT Jones, SM Kandathil - Bioinformatics, 2018 - academic.oup.com
Motivation In addition to substitution frequency data from protein sequence alignments,
many state-of-the-art methods for contact prediction rely on additional sources of …
many state-of-the-art methods for contact prediction rely on additional sources of …
From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction
Various approaches have explored the covariation of residues in multiple-sequence
alignments of homologous proteins to extract functional and structural information. Among …
alignments of homologous proteins to extract functional and structural information. Among …
Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction
The prospect of identifying contacts in protein structures purely from aligned protein
sequences has lured researchers for a long time, but progress has been modest until …
sequences has lured researchers for a long time, but progress has been modest until …
Genetically modified proteins: functional improvement and chimeragenesis
L Balabanova, V Golotin, A Podvolotskaya… - …, 2015 - Taylor & Francis
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis
for the functional improvement of proteins in areas where traditional protein engineering …
for the functional improvement of proteins in areas where traditional protein engineering …
Accurate contact predictions using covariation techniques and machine learning
T Kosciolek, DT Jones - Proteins: Structure, Function, and …, 2016 - Wiley Online Library
Here we present the results of residue–residue contact predictions achieved in CASP11 by
the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On …
the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On …
Covariation is a poor measure of molecular coevolution
Recent developments in the analysis of amino acid covariation are leading to breakthroughs
in protein structure prediction, protein design, and prediction of the interactome. It is …
in protein structure prediction, protein design, and prediction of the interactome. It is …
The tangled bank of amino acids
RA Goldstein, DD Pollock - Protein Science, 2016 - Wiley Online Library
The use of amino acid substitution matrices to model protein evolution has yielded important
insights into both the evolutionary process and the properties of specific protein families. In …
insights into both the evolutionary process and the properties of specific protein families. In …
A large-scale comparative assessment of methods for residue–residue contact prediction
Sequence-based prediction of residue–residue contact in proteins becomes increasingly
more important for improving protein structure prediction in the big data era. In this study, we …
more important for improving protein structure prediction in the big data era. In this study, we …
Co-evolution of intrinsically disordered proteins with folded partners witnessed by evolutionary couplings
Although improved strategies for the detection and analysis of evolutionary couplings (ECs)
between protein residues already enable the prediction of protein structures and …
between protein residues already enable the prediction of protein structures and …