Research graph
References from Research progress of reduced amino acid alphabets in protein analysis and prediction. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1146/annurev-anchem-071213-020216
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10.1093/chromsci/bmw167
10.1093/chromsci/bmw167 · External reference
10.1016/j.pbiomolbio.2019.09.004
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Deep learning in proteomics
10.1002/pmic.201900335 · 2020 · External reference
10.1016/j.compbiomed.2020.103667
10.1016/j.compbiomed.2020.103667 · External reference
DFpin: Deep learning-based protein-binding site prediction with feature-based non-redundancy from RNA level
10.1016/j.compbiomed.2022.105216 · 2022 · External reference
Protein contact map prediction based on ResNet and DenseNet
10.1155/2020/7584968 · 2020 · External reference
10.1007/978-1-62703-658-0_11
10.1007/978-1-62703-658-0_11 · External reference
STatistical Inference Relief (STIR) feature selection
10.1093/bioinformatics/bty788 · 2019 · External reference
10.1016/j.omtn.2020.02.004
10.1016/j.omtn.2020.02.004 · External reference
Linear discriminant analysis identifies mitochondrially localized proteins in Neurospora crassa
10.1021/acs.jproteome.5b00329 · 2015 · External reference
10.1177/1176934319867088
10.1177/1176934319867088 · External reference
IHEC_RAAC: a online platform for identifying human enzyme classes via reduced amino acid cluster strategy
10.1007/s00726-021-02941-9 · 2021 · External reference
RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule
10.1093/database/baz131 · 2019 · External reference
Identification of disease-related 2-oxoglutarate/Fe (II)-dependent oxygenase based on reduced amino acid cluster strategy
10.3389/fcell.2021.707938 · 2021 · External reference
Polypeptides. 53. Water-soluble copolypeptides of L-glutamic acid, L-lysine, and L-alanine
10.1002/bip.1967.360050304 · 1967 · External reference
Folding and function of a T4 lysozyme containing 10 consecutive alanines illustrate the redundancy of information in an amino acid sequence
10.1073/pnas.89.9.3751 · 1992 · External reference
10.1128/mr.56.1.229-264.1992
10.1128/mr.56.1.229-264.1992 · External reference
10.1038/nsb1097-805
10.1038/nsb1097-805 · External reference
As simple as can be?
10.1038/nsb1197-871 · 1997 · External reference
10.1038/nsb1297-1039
10.1038/nsb1297-1039 · External reference
A computational approach to simplifying the protein folding alphabet
10.1038/14918 · 1999 · External reference
A new substitution matrix for protein sequence searches based on contact frequencies in protein structures
10.1093/protein/6.3.267 · 1993 · External reference
10.1073/pnas.89.22.10915
10.1073/pnas.89.22.10915 · External reference
Using BLOSUM in sequence alignments
2008 · External reference
Using PAM Matrices in Sequence Alignments
2008 · External reference
Comparison of the PAM and BLOSUM amino acid substitution matrices
2008 · External reference
The rapid generation of mutation data matrices from protein sequences
1992 · External reference
10.1093/oxfordjournals.molbev.a003851
10.1093/oxfordjournals.molbev.a003851 · External reference
10.1093/protein/13.3.149
10.1093/protein/13.3.149 · External reference
10.1016/j.jtbi.2003.12.010
10.1016/j.jtbi.2003.12.010 · External reference
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
10.1093/bioinformatics/18.8.1102 · 2002 · External reference
10.1073/pnas.222243999
10.1073/pnas.222243999 · External reference
Optimizing amino acid groupings for GPCR classification
10.1093/bioinformatics/btn382 · 2008 · External reference
The nature of statistical learning theory∼
10.1109/tnn.1997.641482 · 1997 · External reference
Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
10.1016/j.febslet.2004.09.036 · 2004 · External reference
Automated alphabet reduction for protein datasets
10.1186/1471-2105-10-6 · 2009 · External reference
Protein subcellular localization prediction based on reduced representation of amino acid and statistical characteristic
2015 · External reference
Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks
10.1007/s008940100038 · 2001 · External reference
cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks
10.1002/prot.25966 · 2020 · External reference
RAPSearch: a fast protein similarity search tool for short reads
10.1186/1471-2105-12-159 · 2011 · External reference
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
10.1093/bioinformatics/btr595 · 2011 · External reference
10.1038/nmeth.3176
10.1038/nmeth.3176 · External reference
10.1038/s41467-018-04964-5
10.1038/s41467-018-04964-5 · External reference
10.1038/nbt.3988
10.1038/nbt.3988 · External reference
Fast and sensitive taxonomic assignment to metagenomic contigs
10.1093/bioinformatics/btab184 · 2021 · External reference
Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets
10.1002/prot.20881 · 2006 · External reference
10.1016/j.jtbi.2006.11.010
10.1016/j.jtbi.2006.11.010 · External reference
Prediction of ketoacyl synthase family using reduced amino acid alphabets
10.1007/s10295-011-1047-z · 2012 · External reference
iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
10.1016/j.ab.2013.05.024 · 2013 · External reference
iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition
10.1371/journal.pone.0106691 · 2014 · External reference
Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet
10.1016/j.peptides.2009.06.032 · 2009 · External reference
Predicting the types of J-proteins using clustered amino acids
10.1155/2014/935719 · 2014 · External reference
iDPF-PseRAAAC: a web-server for identifying the defensin peptide family and subfamily using pseudo reduced amino acid alphabet composition
10.1371/journal.pone.0145541 · 2015 · External reference
10.1093/bioinformatics/bty179
10.1093/bioinformatics/bty179 · External reference
POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix
10.1093/bioinformatics/btm330 · 2007 · External reference
PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition
10.1093/bioinformatics/btw564 · 2017 · External reference
10.1016/j.biosystems.2019.03.002
10.1016/j.biosystems.2019.03.002 · External reference
RaacLogo: a new sequence logo generator by using reduced amino acid clusters
10.1093/bib/bbaa096 · 2021 · External reference
iSP-RAAC: identify secretory proteins of malaria parasite using reduced amino acid composition
10.2174/1386207323666200402084518 · 2020 · External reference
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
10.1093/nar/gkl305 · 2006 · External reference
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets
2022 · External reference
10.1007/s00249-007-0188-5
10.1007/s00249-007-0188-5 · External reference
10.1007/s00894-013-1916-7
10.1007/s00894-013-1916-7 · External reference
10.1007/s11427-007-0023-3
10.1007/s11427-007-0023-3 · External reference
Relations between chemical structure and biological activity in peptides
10.1016/0022-5193(66)90112-3 · 1966 · External reference
10.1073/pnas.0408677102
10.1073/pnas.0408677102 · External reference
A new approach to clustering the amino acids
10.1006/jtbi.1996.0213 · 1996 · External reference
10.1006/jmbi.2001.4908
10.1006/jmbi.2001.4908 · External reference
10.1002/prot.10442
10.1002/prot.10442 · External reference
Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition
10.1016/j.jtbi.2008.11.003 · 2009 · External reference
Structure-derived substitution matrices for alignment of distantly related sequences
10.1093/protein/13.8.545 · 2000 · External reference
Simplified amino acid alphabets based on deviation of conditional probability from random background
10.1103/physreve.66.021906 · 2002 · External reference
Distance-dependent classification of amino acids by information theory
10.1002/prot.22744 · 2010 · External reference
Amino acid partitioning using a Fiedler vector model
10.1007/s00249-007-0182-y · 2007 · External reference
10.1093/molbev/msm144
10.1093/molbev/msm144 · External reference
Reduction of protein sequence complexity by residue grouping
2003 · External reference
Unearthing the root of amino acid similarity
10.1007/s00239-013-9565-0 · 2013 · External reference
Amino acid classes and the protein folding problem
10.1063/1.1333025 · 2001 · External reference
A general clustering approach with application to the Miyazawa-Jernigan potentials for amino acids
10.1002/prot.10570 · 2004 · External reference
Automatic generation of primary sequence patterns from sets of related protein sequences
10.1073/pnas.87.1.118 · 1990 · External reference
10.1007/s00726-014-1817-9
10.1007/s00726-014-1817-9 · External reference
An iterative method for extracting energy-like quantities from protein structures
10.1073/pnas.93.21.11628 · 1996 · External reference
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function
10.1006/jmbi.1999.2911 · 1999 · External reference
10.1016/0022-2836(92)90228-c
10.1016/0022-2836(92)90228-c · External reference
10.1016/j.jtbi.2003.09.009
10.1016/j.jtbi.2003.09.009 · External reference
Predicting disordered regions in proteins based on decision trees of reduced amino acid composition
10.1089/cmb.2006.13.1723 · 2006 · External reference
10.1186/1759-2208-5-1
10.1186/1759-2208-5-1 · External reference
Unresolved reference
External reference
10.1002/(sici)1097-0134(20000201)38:2<149::aid-prot4>3.0.co;2-#
10.1002/(sici)1097-0134(20000201)38:2<149::aid-prot4>3.0.co;2-# · External reference
10.1002/prot.24936
10.1002/prot.24936 · External reference
Conformational properties of amino acid residues in globular proteins
10.1016/s0022-2836(76)80008-3 · 1976 · External reference
10.1002/prot.20648
10.1002/prot.20648 · External reference
