Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Authors
Keywords
Membrane proteins, Protein structure prediction, Neural networks, Protein structure, Forecasting, Multiple alignment calculation, Convolution, Protein structure databases
Journal
PLoS Computational Biology
Volume 13, Issue 1, Pages e1005324
Publisher
Public Library of Science (PLoS)
Online
2017-01-10
DOI
10.1371/journal.pcbi.1005324
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
- (2016) Sheng Wang et al. Scientific Reports
- Deep learning
- (2015) Yann LeCun et al. NATURE
- The Phyre2 web portal for protein modeling, prediction and analysis
- (2015) Lawrence A Kelley et al. Nature Protocols
- CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
- (2014) Stefan Seemayer et al. BIOINFORMATICS
- MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
- (2014) David T. Jones et al. BIOINFORMATICS
- Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
- (2014) Magnus Ekeberg et al. JOURNAL OF COMPUTATIONAL PHYSICS
- SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
- (2014) Marco Biasini et al. NUCLEIC ACIDS RESEARCH
- Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
- (2014) Marcin J. Skwark et al. PLoS Computational Biology
- Predicting protein contact map using evolutionary and physical constraints by integer programming
- (2013) Z. Wang et al. BIOINFORMATICS
- Emerging methods in protein co-evolution
- (2013) David de Juan et al. NATURE REVIEWS GENETICS
- Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
- (2013) Magnus Ekeberg et al. PHYSICAL REVIEW E
- Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
- (2013) H. Kamisetty et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Critical assessment of methods of protein structure prediction (CASP) - round x
- (2013) John Moult et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- The Protein Model Portal—a comprehensive resource for protein structure and model information
- (2013) Juergen Haas et al. Database-The Journal of Biological Databases and Curation
- Protein structure alignment beyond spatial proximity
- (2013) Sheng Wang et al. Scientific Reports
- Deep architectures for protein contact map prediction
- (2012) Pietro Di Lena et al. BIOINFORMATICS
- Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups
- (2012) Geoffrey Hinton et al. IEEE SIGNAL PROCESSING MAGAZINE
- Structure of Shroom domain 2 reveals a three-segmented coiled-coil required for dimerization, Rock binding, and apical constriction
- (2012) Swarna Mohan et al. MOLECULAR BIOLOGY OF THE CELL
- Template-based protein structure modeling using the RaptorX web server
- (2012) Morten Källberg et al. Nature Protocols
- PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
- (2011) David T. Jones et al. BIOINFORMATICS
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- (2011) Michael Remmert et al. NATURE METHODS
- Protein 3D Structure Computed from Evolutionary Sequence Variation
- (2011) Debora S. Marks et al. PLoS One
- Direct-coupling analysis of residue coevolution captures native contacts across many protein families
- (2011) F. Morcos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- How significant is a protein structure similarity with TM-score = 0.5?
- (2010) Jinrui Xu et al. BIOINFORMATICS
- Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
- (2010) Marcos R. Betancourt et al. PROTEIN SCIENCE
- A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
- (2008) Sitao Wu et al. BIOINFORMATICS
- Identification of direct residue contacts in protein-protein interaction by message passing
- (2008) M. Weigt et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation