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Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins

https://doi.org/10.1101/379800
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jmbi.1994.1104openalex-snapshot
Hidden Markov Models in Computational Biology
inferredcites →https://doi.org/10.1006/jmbi.1997.1525openalex-snapshot
Empirical statistical estimates for sequence similarity searches
inferredcites →https://doi.org/10.1006/jmbi.1998.2221openalex-snapshot
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
inferredcites →https://doi.org/10.1016/bs.aivir.2017.02.002openalex-snapshot
The Envelope Proteins of the Bunyavirales
inferredcites →https://doi.org/10.1016/j.cell.2014.02.020openalex-snapshot
Structural Basis of Eukaryotic Cell-Cell Fusion
inferredcites →https://doi.org/10.1016/j.cell.2017.01.024openalex-snapshot
The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein
inferredcites →https://doi.org/10.1016/j.cub.2018.01.024openalex-snapshot
Fusogens
inferredcites →https://doi.org/10.1016/j.febslet.2007.01.093openalex-snapshot
Virus membrane fusion
inferredcites →https://doi.org/10.1016/j.jmb.2003.10.025openalex-snapshot
On the Role of Structural Information in Remote Homology Detection and Sequence Alignment: New Methods Using Hybrid Sequence Profiles
inferredcites →https://doi.org/10.1016/j.jmb.2004.03.016openalex-snapshot
A Combined Transmembrane Topology and Signal Peptide Prediction Method
inferredcites →https://doi.org/10.1016/j.sbi.2005.04.003openalex-snapshot
Predicting protein function from sequence and structural data
inferredcites →https://doi.org/10.1016/j.sbi.2009.04.003openalex-snapshot
Advances and pitfalls of protein structural alignment
inferredcites →https://doi.org/10.1016/j.virol.2015.03.043openalex-snapshot
Viral membrane fusion
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nrg1838openalex-snapshot
An integrated view of protein evolution
inferredcites →https://doi.org/10.1038/nrm2281openalex-snapshot
Predicting protein function from sequence and structure
inferredcites →https://doi.org/10.1038/nrmicro1326openalex-snapshot
Virus membrane-fusion proteins: more than one way to make a hairpin
inferredcites →https://doi.org/10.1080/10409230802058320openalex-snapshot
Structures and Mechanisms of Viral Membrane Fusion Proteins: Multiple Variations on a Common Theme
inferredcites →https://doi.org/10.1089/10665270152530845openalex-snapshot
Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models
inferredcites →https://doi.org/10.1089/cmb.2010.0328openalex-snapshot
Sequence Alignment as Hypothesis Testing
inferredcites →https://doi.org/10.1093/bib/bbk001openalex-snapshot
Statistical significance in biological sequence analysis
inferredcites →https://doi.org/10.1093/bib/bbw108openalex-snapshot
A comprehensive review and comparison of different computational methods for protein remote homology detection
inferredcites →https://doi.org/10.1093/bioinformatics/13.2.191openalex-snapshot
Scoring hidden Markov models
inferredcites →https://doi.org/10.1093/bioinformatics/14.10.846openalex-snapshot
Hidden Markov models for detecting remote protein homologies.
inferredcites →https://doi.org/10.1093/bioinformatics/14.9.755openalex-snapshot
Profile hidden Markov models.
inferredcites →https://doi.org/10.1093/bioinformatics/7.1.1openalex-snapshot
Fast optimal alignment
inferredcites →https://doi.org/10.1093/bioinformatics/bti125openalex-snapshot
Protein homology detection by HMM–HMM comparison
inferredcites →https://doi.org/10.1093/bioinformatics/bti629openalex-snapshot
Calibrating E-values for hidden Markov models using reverse-sequence null models
inferredcites →https://doi.org/10.1093/bioinformatics/bts618openalex-snapshot
Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity
inferredcites →https://doi.org/10.1093/bioinformatics/btw752openalex-snapshot
The structural bioinformatics library: modeling in biomolecular science and beyond
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gki414openalex-snapshot
ProFunc: a server for predicting protein function from 3D structure
inferredcites →https://doi.org/10.1093/nar/gkr1178openalex-snapshot
The NCBI Taxonomy database
inferredcites →https://doi.org/10.1093/nar/gkr367openalex-snapshot
HMMER web server: interactive sequence similarity searching
inferredcites →https://doi.org/10.1093/nar/gks362openalex-snapshot
CSA: comprehensive comparison of pairwise protein structure alignments
inferredcites →https://doi.org/10.1101/379768openalex-snapshot
Multiscale analysis of structurally conserved motifs
inferredcites →https://doi.org/10.1146/annurev-virology-031413-085521openalex-snapshot
Mechanisms of Virus Membrane Fusion Proteins
inferredcites →https://doi.org/10.1371/journal.pbio.2006357openalex-snapshot
Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes
inferredcites →https://doi.org/10.1371/journal.pcbi.1000069openalex-snapshot
A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
inferredcites →https://doi.org/10.2174/138920306777452312openalex-snapshot
Advances in Homology Protein Structure Modeling
inferredcites →https://doi.org/10.2202/1544-6115.1585openalex-snapshot
Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn
inferredcites →https://doi.org/10.5860/choice.41-4039openalex-snapshot
Bioinformatics and functional genomics

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inferred← citeshttps://doi.org/10.1101/379768openalex-snapshot
Multiscale analysis of structurally conserved motifs
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