[HTML][HTML] Deep learning methods in protein structure prediction

M Torrisi, G Pollastri, Q Le - Computational and Structural Biotechnology …, 2020 - Elsevier
Abstract Protein Structure Prediction is a central topic in Structural Bioinformatics. Since
the'60s statistical methods, followed by increasingly complex Machine Learning and recently …

Deep mutational scanning: a new style of protein science

DM Fowler, S Fields - Nature methods, 2014 - nature.com
Mutagenesis provides insight into proteins, but only recently have assays that couple
genotype to phenotype been used to assess the activities of as many as 1 million mutant …

Evaluating protein transfer learning with TAPE

R Rao, N Bhattacharya, N Thomas… - Advances in neural …, 2019 - proceedings.neurips.cc
Protein modeling is an increasingly popular area of machine learning research. Semi-
supervised learning has emerged as an important paradigm in protein modeling due to the …

Machine learning-assisted directed protein evolution with combinatorial libraries

Z Wu, SBJ Kan, RD Lewis… - Proceedings of the …, 2019 - National Acad Sciences
To reduce experimental effort associated with directed protein evolution and to explore the
sequence space encoded by mutating multiple positions simultaneously, we incorporate …

Accurate de novo prediction of protein contact map by ultra-deep learning model

S Wang, S Sun, Z Li, R Zhang, J Xu - PLoS computational biology, 2017 - journals.plos.org
Motivation Protein contacts contain key information for the understanding of protein structure
and function and thus, contact prediction from sequence is an important problem. Recently …

Protein structure determination using metagenome sequence data

S Ovchinnikov, H Park, N Varghese, PS Huang… - Science, 2017 - science.org
Despite decades of work by structural biologists, there are still~ 5200 protein families with
unknown structure outside the range of comparative modeling. We show that Rosetta …

Assessment of contact predictions in CASP12: co‐evolution and deep learning coming of age

J Schaarschmidt, B Monastyrskyy… - Proteins: Structure …, 2018 - Wiley Online Library
Following up on the encouraging results of residue‐residue contact prediction in the
CASP11 experiment, we present the analysis of predictions submitted for CASP12. The …

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 …

Large-scale determination of previously unsolved protein structures using evolutionary information

S Ovchinnikov, L Kinch, H Park, Y Liao, J Pei, DE Kim… - elife, 2015 - elifesciences.org
The prediction of the structures of proteins without detectable sequence similarity to any
protein of known structure remains an outstanding scientific challenge. Here we report …

Three-dimensional protein structure prediction: Methods and computational strategies

M Dorn, MB e Silva, LS Buriol, LC Lamb - Computational biology and …, 2014 - Elsevier
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …