Practical limits of function prediction

scientific article published on 01 October 2000

Practical limits of function prediction is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1002/1097-0134(20001001)41:1<98::AID-PROT120>3.0.CO;2-S
P698PubMed publication ID10944397

P2093author name stringValencia A
Devos D
P433issue1
P304page(s)98-107
P577publication date2000-10-01
P1433published inProteinsQ7251514
P1476titlePractical limits of function prediction
P478volume41

Reverse relations

cites work (P2860)
Q39773780A computational strategy for protein function assignment which addresses the multidomain problem.
Q30401235A new approach to assess and predict the functional roles of proteins across all known structures
Q33246840A new measure for functional similarity of gene products based on Gene Ontology
Q38414582A semantic analysis of the annotations of the human genome
Q33217257A sentence sliding window approach to extract protein annotations from biomedical articles
Q38508638A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions
Q35165240A structural perspective on genome evolution
Q34731493A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
Q34093494A tour of structural genomics.
Q33549705Accuracy of protein-protein binding sites in high-throughput template-based modeling
Q34569638Accurate prediction of protein enzymatic class by N-to-1 Neural Networks
Q29048144An analysis of the Sargasso Sea resource and the consequences for database composition
Q36268840An improved method for functional similarity analysis of genes based on Gene Ontology
Q40415523Annotation transfer for genomics: measuring functional divergence in multi-domain proteins
Q33187609Approach of the functional evolution of duplicated genes in Saccharomyces cerevisiae using a new classification method based on protein-protein interaction data.
Q34247968Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.
Q37570934Automated prediction of protein function and detection of functional sites from structure
Q33294652Automated protein subfamily identification and classification
Q43561238Automatic annotation of protein function based on family identification
Q25255690Automatic discovery of cross-family sequence features associated with protein function.
Q42293187Automatic single- and multi-label enzymatic function prediction by machine learning
Q31039895BLAST-based structural annotation of protein residues using Protein Data Bank.
Q36294114Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery
Q30332613Bioinformatics methods to predict protein structure and function. A practical approach.
Q37141790Bridging protein local structures and protein functions
Q38463316CATH FunFHMMer web server: protein functional annotations using functional family assignments
Q39087712Cell-penetrating fusion peptides OD1 and OD2 interact with Bcr-Abl and influence the growth and apoptosis of K562 cells
Q37424495Challenges in the computational design of proteins
Q34284958CombFunc: predicting protein function using heterogeneous data sources
Q30604355Combining heterogeneous data sources for accurate functional annotation of proteins.
Q33523795Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families
Q36640722Comparing function and structure between entire proteomes
Q46279817Complex evolutionary relationships among four classes of modular RNA-binding splicing regulators in eukaryotes: the hnRNP, SR, ELAV-like and CELF proteins
Q24797455Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1
Q39501240Computational prediction of protein function based on weighted mapping of domains and GO terms
Q34628467Concomitant prediction of function and fold at the domain level with GO-based profiles
Q41140874Cutoff lensing: predicting catalytic sites in enzymes
Q33868610De novo transcriptome analysis shows differential expression of genes in salivary glands of edible bird's nest producing swiftlets
Q34331168De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system.
Q33332182De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features
Q33821576Detecting remotely related proteins by their interactions and sequence similarity
Q28649315Determining similarity of scientific entities in annotation datasets
Q33960336Did evolution leap to create the protein universe?
Q64118033Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space
Q117928031Diversity of Xanthoparmelia (Parmeliaceae) species in Mexican xerophytic scrub vegetation, evidenced by molecular, morphological and chemistry data
Q30361712Efficient identification of critical residues based only on protein structure by network analysis.
Q36420036Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines
Q33486721Enzyme classification with peptide programs: a comparative study.
Q30330428Enzyme function less conserved than anticipated.
Q24801595Evidence for existence of thirty hypothetical proteins in rat brain
Q33959976Evolution of enzymes in metabolism: a network perspective.
Q51730985Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.
Q42623329Evolutionary constraints on structural similarity in orthologs and paralogs
Q28744539Evolutionary innovations and the organization of protein functions in genotype space
Q38446573Exhaustive comparison and classification of ligand-binding surfaces in proteins
Q29036401Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
Q30416918Exploring protein dynamics space: the dynasome as the missing link between protein structure and function
Q29614387Finding nuclear localization signals
Q37419187Finding of residues crucial for supersecondary structure formation
Q48089439FlgM anti-sigma factors: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships
Q24814930Functional coverage of the human genome by existing structures, structural genomics targets, and homology models
Q33687254GOPred: GO molecular function prediction by combined classifiers
Q34915863Gene ontology function prediction in mollicutes using protein-protein association networks
Q46245936Global computational mutagenesis provides a critical stability framework in protein structures
Q33562611HangOut: generating clean PSI-BLAST profiles for domains with long insertions
Q55357639Harnessing the evolutionary information on oxygen binding proteins through Support Vector Machines based modules.
Q52956083How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity?
Q42624769Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of Brachiaria brizantha
Q43055480Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
Q43749943Inferring functional relationships of proteins from local sequence and spatial surface patterns
Q28552164Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
Q24803312JEvTrace: refinement and variations of the evolutionary trace in JAVA
Q28728482KB-Rank: efficient protein structure and functional annotation identification via text query
Q35165255Ligand binding: functional site location, similarity and docking
Q30362636Ligation site in proteins recognized in silico.
Q33327771Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio
Q30360755Localization of ligand binding site in proteins identified in silico.
Q52942751Loopy proteins appear conserved in evolution.
Q35082625Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads
Q36908271Metabolic innovations towards the human lineage
Q33332013Metrics for GO based protein semantic similarity: a systematic evaluation
Q87518326Modeling sequence and function similarity between proteins for protein functional annotation
Q33649790More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology
Q30764897Motif-based fold assignment
Q45118089Overexpression of Populus trichocarpa Mitogen-Activated Protein Kinase Kinase4 Enhances Salt Tolerance in Tobacco
Q34530521PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset
Q36220729PROPER: global protein interaction network alignment through percolation matching.
Q33309502Predicting gene ontology functions from protein's regional surface structures
Q38375823Predicting novel human gene ontology annotations using semantic analysis
Q52012972Predicting reliable regions in protein alignments from sequence profiles.
Q37318147Predicting the nuclear localization signals of 107 types of HPV L1 proteins by bioinformatic analysis
Q30557389Prediction and experimental validation of enzyme substrate specificity in protein structures
Q30002391Prediction of Human Protein Function from Post-translational Modifications and Localization Features
Q30367104Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.
Q33337959Prediction of enzyme function by combining sequence similarity and protein interactions
Q33285864Prediction of functional sites based on the fuzzy oil drop model
Q36519515Prediction of functional sites by analysis of sequence and structure conservation
Q51898836Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm.
Q106645059Prediction of protein function using a deep convolutional neural network ensemble
Q33184404PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA
Q25255113Probabilistic annotation of protein sequences based on functional classifications.
Q27940324Probabilistic approach to predicting substrate specificity of methyltransferases
Q36914675Protein co-evolution, co-adaptation and interactions
Q39808508Protein families and TRIBES in genome sequence space
Q35165260Protein informatics towards function identification
Q34365175Protein interaction databases
Q30492816Protein interactions and ligand binding: from protein subfamilies to functional specificity
Q24814913Protein molecular function prediction by Bayesian phylogenomics
Q37389046Protein promiscuity and its implications for biotechnology
Q30407238Quantification of protein group coherence and pathway assignment using functional association
Q33290341Quantitative assessment of relationship between sequence similarity and function similarity
Q33560370Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds
Q33293617Quantitative sequence-function relationships in proteins based on gene ontology
Q39555761SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
Q43103662SARA: a server for function annotation of RNA structures
Q30000951Scoring protein relationships in functional interaction networks predicted from sequence data
Q47423196Sequence and structural differences between enzyme and nonenzyme homologs
Q36639642Sequence conserved for subcellular localization
Q30002311Sequence-based feature prediction and annotation of proteins
Q35806623Structural characterization of the human proteome.
Q35204026Structural genomics: computational methods for structure analysis
Q30488546Structural motifs recurring in different folds recognize the same ligand fragments
Q27640210Structures of phosphate and trivanadate complexes of Bacillus stearothermophilus phosphatase PhoE: structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily
Q30370436The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone
Q34983597The relationship between gene isoform multiplicity, number of exons and protein divergence
Q33381576The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
Q27027251The use of evolutionary patterns in protein annotation
Q30844251The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines
Q42650864Tolerance analysis of chloroplast OsCu/Zn-SOD overexpressing rice under NaCl and NaHCO3 stress.
Q33281289Towards complete sets of farnesylated and geranylgeranylated proteins
Q36088352Transmembrane helix: simple or complex
Q35208620UniqueProt: Creating representative protein sequence sets
Q47612852Using a neural network and spatial clustering to predict the location of active sites in enzymes
Q41357141VICMpred: an SVM-based method for the prediction of functional proteins of Gram-negative bacteria using amino acid patterns and composition.
Q24814545Variation in structural location and amino acid conservation of functional sites in protein domain families
Q28554445Xenobiotic Metabolism and Gut Microbiomes
Q35914235firestar--prediction of functionally important residues using structural templates and alignment reliability

Search more.