Using structural motif templates to identify proteins with DNA binding function

scientific article published in June 2003

Using structural motif templates to identify proteins with DNA binding function is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1093/NAR/GKG386
P932PMC publication ID156721
P698PubMed publication ID12771208
P5875ResearchGate publication ID277389193

P50authorJanet ThorntonQ6153626
Susan JonesQ57034020
Irene NobeliQ57542959
P2093author name stringJonathan A Barker
P2860cites workThe CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis toolsQ24248165
Immunocytochemical localization and crystal structure of human frequenin (neuronal calcium sensor 1)Q24290554
SMART, a simple modular architecture research tool: identification of signaling domainsQ24597380
Basic local alignment search toolQ25938991
Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferaseQ27619727
Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferasesQ27628854
Crystal Structure of Thermotoga maritima 0065, a Member of the IclR Transcriptional Factor FamilyQ27638173
Refined 1.8 A crystal structure of the lambda repressor-operator complexQ27642126
Crystal structure of Thermus aquaticus DNA polymeraseQ27729817
Crystal structure of a yeast TBP/TATA-box complexQ27732067
Structure of Taq polymerase with DNA at the polymerase active siteQ27733244
The Pfam protein families databaseQ27860470
SCOP: a structural classification of proteins database for the investigation of sequences and structuresQ27860689
CATH--a hierarchic classification of protein domain structuresQ27861100
Hidden Markov models for sequence analysis: extension and analysis of the basic methodQ28286314
RASMOL: biomolecular graphics for allQ29547757
DNA polymerases: structural diversity and common mechanismsQ29619403
The helix-turn-helix DNA binding motifQ34045093
PROSITE: a dictionary of sites and patterns in proteinsQ35921056
Highly specific protein sequence motifs for genome analysisQ36252448
A structural taxonomy of DNA-binding domainsQ37483850
Investigation of the Role of Tyrosine-114 in the Activity of Human O6-Alkylguanine-DNA AlkyltranferaseQ38333607
Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipasesQ42136534
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sitesQ42562234
Protein-DNA interactions: A structural analysisQ42600123
Profile analysisQ43640346
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificityQ47615859
Mining protein sequences for motifsQ78678506
P433issue11
P407language of work or nameEnglishQ1860
P304page(s)2811-2823
P577publication date2003-06-01
P1433published inNucleic Acids ResearchQ135122
P1476titleUsing structural motif templates to identify proteins with DNA binding function
P478volume31

Reverse relations

cites work (P2860)
Q34058424A structural-alphabet-based strategy for finding structural motifs across protein families.
Q39300811An evolution-based DNA-binding residue predictor using a dynamic query-driven learning scheme
Q35380883An overview of the prediction of protein DNA-binding sites
Q30371533Classifying RNA-binding proteins based on electrostatic properties
Q40640989DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
Q30376355DNA-Prot: identification of DNA binding proteins from protein sequence information using random forest.
Q24796955Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information
Q38603466EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation.
Q53408509Energy-based prediction of amino acid-nucleotide base recognition
Q30378289Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.
Q40068041Identifying DNA-binding proteins using structural motifs and the electrostatic potential
Q24817122Kernel-based machine learning protocol for predicting DNA-binding proteins
Q41010993PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins.
Q60923448PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine
Q35773099Polyanions and the proteome
Q93012384PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity
Q35162327Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.
Q64230286Prediction of RNA- and DNA-Binding Proteins Using Various Machine Learning Classifiers
Q39940236Prediction of interactiveness of proteins and nucleic acids based on feature selections
Q24812633ProFunc: a server for predicting protein function from 3D structure
Q33352065Protein-DNA interactions: the story so far and a new method for prediction
Q30360004Towards fully automated structure-based function prediction in structural genomics: a case study
Q30336320Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
Q92283019iProDNA-CapsNet: identifying protein-DNA binding residues using capsule neural networks

Search more.