Pfam

swMATH23108MaRDI QIDQ34892FDOQ34892

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Official website: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347511/

Cited In (only showing first 100 items - show all)

• Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix
• A hidden Markov model applied to the protein 3D structure analysis
• An efficient genomic signature ranking method for genomic island prediction from a single genome
• Variational Bayes via propositionalized probability computation in PRISM
• Refining cellular pathway models using an ensemble of heterogeneous data sources
• ECS: an automatic enzyme classifier based on functional domain composition
• Sequence annotation with HMMs: new problems and their complexity
• The first peptides: the evolutionary transition between prebiotic amino acids and early proteins
• Computation of mutual information from hidden Markov models
• Neighborhood functions and hill-climbing strategies dedicated to the generalized ungapped local multiple alignment
• MoDEL: an efficient strategy for ungapped local multiple alignment
• Automatic topography of high-dimensional data sets by non-parametric density peak clustering
• Discovering short linear protein motif based on selective training of profile hidden Markov models
• Towards a comprehensive collection of diagnostic patterns for protein sequence classification
• Fast embedding methods for clustering tens of thousands of sequences
• Cooperative ``folding transition in the sequence space facilitates function-driven evolution of protein families
• Comparative protein structure modeling in genomics
• Protein model refinement using structural fragment tessellation
• Potential drug targets in Mycobacterium tuberculosis through metabolic pathway analysis
• A matrix based algorithm for protein-protein interaction prediction using domain-domain associations
• The iProClass integrated database for protein functional analysis
• On application of directons to functional classification of genes in prokaryotes
• Analyzing functional similarity of protein sequences with discrete wavelet transform
• The metabolic pH response in Lactococcus lactis: An integrative experimental and modelling approach
• Non-linear models based on simple topological indices to identify RNase III protein members
• Protein domain hierarchy Gibbs sampling strategies
• Operon prediction based on SVM
• The EM algorithm and the rise of computational biology
• Mathematical basis of improved protein subfamily classification by a HMM-based sequence filter
• A proteome-wide analysis of domain architectures of prokaryotic single-spanning transmembrane proteins
• Construction and characterization of a rock-cluster-based EST analysis pipeline
• Bioinformatics. Volume II: structure, function, and applications
• Statistical correction for functional metagenomic profiling of a microbial community with short NGS reads
• Analysis of expression profile and gene variation via development of methods for next generation sequencing data
• Predicting DNA binding proteins using support vector machine with hybrid fractal features
• SVM-Prot
• Pattern-constrained multiple polypeptide sequence alignment
• Applications of domain-domain interactions in pathway study
• A hybrid method for protein sequence modeling with improved accuracy
• \textit{In silico} analysis of \textit{plasmodium falciparum} CDPK5 protein through molecular modeling, docking and dynamics
• Fast error-tolerant quartet phylogeny algorithms
• Compressing table data with column dependency
• Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference
• Approximate symbolic pattern matching for protein sequence data
• Fast detection of common sequence structure patterns in RNAs
• On the entropy of protein families
• Elman RNN based classification of proteins sequences on account of their mutual information
• A hyper-heuristic for the longest common subsequence problem
• The consensus string problem and the complexity of comparing hidden Markov models.
• Predicting protein fold pattern with functional domain and sequential evolution information
• Some remarks on protein attribute prediction and pseudo amino acid composition
• TRANSPATH
• BioProspector
• Nomad
• mpiBLAST
• Cluster-C
• GOstat
• Psortb
• 3DCoffee
• ClustalW
• DIALIGN
• SMART
• BLAST
• LTR_FINDER
• MUSCLE
• BioGRID
• KEGG
• FASTA3
• Rose
• AUTO-MUTE
• FUGUE
• ELM
• PROCHECK
• AutoFACT
• PSICOV
• GeneMark
• INCLUSive
• PartTree
• HHpred
• Profunc
• InterProScan
• PSI-BLAST
• PROSITE
• TRANSFAC
• SWISS-MODEL
• Some operations research methods for analyzing protein sequences and structures
• COMPASS
• PconsC
• IntAct
• UniProt
• ChEMBL
• Jalview
• PANTHER
• MetaSim
• ExonHunter
• DrugBank
• PAGE
• ONE
• PIPE
• zt

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