Matches in DBpedia 2016-04 for { <http://dbpedia.org/resource/Homology_modeling> ?p ?o }
- Homology_modeling abstract "Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the \"target\" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the \"template\"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.".
- Homology_modeling thumbnail DHRS7B_homology_model.png?width=300.
- Homology_modeling wikiPageExternalLink whatif.
- Homology_modeling wikiPageExternalLink swift.cmbi.ru.nl.
- Homology_modeling wikiPageExternalLink pdbreport.
- Homology_modeling wikiPageExternalLink whatcheck.
- Homology_modeling wikiPageID "7026278".
- Homology_modeling wikiPageLength "42952".
- Homology_modeling wikiPageOutDegree "134".
- Homology_modeling wikiPageRevisionID "697311672".
- Homology_modeling wikiPageWikiLink ATPase.
- Homology_modeling wikiPageWikiLink Active_site.
- Homology_modeling wikiPageWikiLink Alpha_and_beta_carbon.
- Homology_modeling wikiPageWikiLink Amino_acid.
- Homology_modeling wikiPageWikiLink Aqueous_solution.
- Homology_modeling wikiPageWikiLink Arginine.
- Homology_modeling wikiPageWikiLink Artificial_neural_network.
- Homology_modeling wikiPageWikiLink BLAST.
- Homology_modeling wikiPageWikiLink Benchmarking.
- Homology_modeling wikiPageWikiLink Binding_site.
- Homology_modeling wikiPageWikiLink Biomolecular_structure.
- Homology_modeling wikiPageWikiLink CAFASP.
- Homology_modeling wikiPageWikiLink CASP.
- Homology_modeling wikiPageWikiLink CHARMM.
- Homology_modeling wikiPageWikiLink Cartesian_coordinate_system.
- Homology_modeling wikiPageWikiLink Category:Bioinformatics.
- Homology_modeling wikiPageWikiLink Category:Protein_methods.
- Homology_modeling wikiPageWikiLink Category:Protein_structure.
- Homology_modeling wikiPageWikiLink Chemical_polarity.
- Homology_modeling wikiPageWikiLink Conformational_isomerism.
- Homology_modeling wikiPageWikiLink Conjugate_gradient_method.
- Homology_modeling wikiPageWikiLink Conserved_sequence.
- Homology_modeling wikiPageWikiLink Cryo-electron_microscopy.
- Homology_modeling wikiPageWikiLink De_novo_protein_structure_prediction.
- Homology_modeling wikiPageWikiLink Deletion_(genetics).
- Homology_modeling wikiPageWikiLink Dihedral_angle.
- Homology_modeling wikiPageWikiLink Discrete_optimized_protein_energy.
- Homology_modeling wikiPageWikiLink Docking_(molecular).
- Homology_modeling wikiPageWikiLink Drug_design.
- Homology_modeling wikiPageWikiLink Effective_Force_Field.
- Homology_modeling wikiPageWikiLink Electron_density.
- Homology_modeling wikiPageWikiLink Electrostatics.
- Homology_modeling wikiPageWikiLink Energy_landscape.
- Homology_modeling wikiPageWikiLink Evolution.
- Homology_modeling wikiPageWikiLink Extended_Vector_Animation.
- Homology_modeling wikiPageWikiLink FASTA.
- Homology_modeling wikiPageWikiLink Force_field_(chemistry).
- Homology_modeling wikiPageWikiLink Gene.
- Homology_modeling wikiPageWikiLink Genetic_drift.
- Homology_modeling wikiPageWikiLink Genome.
- Homology_modeling wikiPageWikiLink Global_distance_test.
- Homology_modeling wikiPageWikiLink Global_optimization.
- Homology_modeling wikiPageWikiLink Globular_protein.
- Homology_modeling wikiPageWikiLink Hydrophobic_effect.
- Homology_modeling wikiPageWikiLink Implicit_solvation.
- Homology_modeling wikiPageWikiLink Insertion_(genetics).
- Homology_modeling wikiPageWikiLink Ion.
- Homology_modeling wikiPageWikiLink List_of_protein_structure_prediction_software.
- Homology_modeling wikiPageWikiLink LiveBench.
- Homology_modeling wikiPageWikiLink Loop_modeling.
- Homology_modeling wikiPageWikiLink Lysine.
- Homology_modeling wikiPageWikiLink MODELLER.
- Homology_modeling wikiPageWikiLink Machine_learning.
- Homology_modeling wikiPageWikiLink Macromolecular_docking.
- Homology_modeling wikiPageWikiLink Mammal.
- Homology_modeling wikiPageWikiLink Membrane_protein.
- Homology_modeling wikiPageWikiLink ModBase.
- Homology_modeling wikiPageWikiLink Molecular_dynamics.
- Homology_modeling wikiPageWikiLink Molecular_mechanics.
- Homology_modeling wikiPageWikiLink Molecular_replacement.
- Homology_modeling wikiPageWikiLink Multiple_sequence_alignment.
- Homology_modeling wikiPageWikiLink Native_state.
- Homology_modeling wikiPageWikiLink Nuclear_magnetic_resonance_spectroscopy.
- Homology_modeling wikiPageWikiLink Nuclear_magnetic_resonance_spectroscopy_of_proteins.
- Homology_modeling wikiPageWikiLink Operon.
- Homology_modeling wikiPageWikiLink Peptide_bond.
- Homology_modeling wikiPageWikiLink Position_weight_matrix.
- Homology_modeling wikiPageWikiLink Potassium.
- Homology_modeling wikiPageWikiLink Probability_density_function.
- Homology_modeling wikiPageWikiLink Protein.
- Homology_modeling wikiPageWikiLink Protein_Data_Bank.
- Homology_modeling wikiPageWikiLink Protein_folding.
- Homology_modeling wikiPageWikiLink Protein_fragment_library.
- Homology_modeling wikiPageWikiLink Protein_structure_prediction.
- Homology_modeling wikiPageWikiLink Protein–protein_interaction.
- Homology_modeling wikiPageWikiLink Protein–protein_interaction_prediction.
- Homology_modeling wikiPageWikiLink Quantum_mechanics.
- Homology_modeling wikiPageWikiLink _software_for_protein_modeling_and_analysis.
- Homology_modeling wikiPageWikiLink Root-mean-square_deviation.
- Homology_modeling wikiPageWikiLink Root-mean-square_deviation_of_atomic_positions.
- Homology_modeling wikiPageWikiLink Saccharomyces_cerevisiae.
- Homology_modeling wikiPageWikiLink Sequence_alignment.
- Homology_modeling wikiPageWikiLink Serine_protease.
- Homology_modeling wikiPageWikiLink Side_chain.
- Homology_modeling wikiPageWikiLink Solvent.
- Homology_modeling wikiPageWikiLink Statistical_potential.
- Homology_modeling wikiPageWikiLink Steric_effects.
- Homology_modeling wikiPageWikiLink Stochastic.
- Homology_modeling wikiPageWikiLink Structural_alignment.
- Homology_modeling wikiPageWikiLink Structural_genomics.