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- Loop_modeling abstract "Loop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from ADP to breast cancer. Because protein function is determined by its shape and the physiochemical properties of its exposed surface, it is important to create an accurate model for protein/ligand interaction studies. The problem arises often in homology modeling, where the tertiary structure of an amino acid sequence is predicted based on a sequence alignment to a template, or a second sequence whose structure is known. Because loops have highly variable sequences even within a given structural motif or protein fold, they often correspond to unaligned regions in sequence alignments; they also tend to be located at the solvent-exposed surface of globular proteins and thus are more conformationally flexible. Consequently, they often cannot be modeled using standard homology modeling techniques. More constrained versions of loop modeling are also used in the data fitting stages of solving a protein structure by X-ray crystallography, because loops can correspond to regions of low electron density and are therefore difficult to resolve.Regions of a structural model that are predicted by non-template-based loop modeling tend to be much less accurate than regions that are predicted using template-based techniques. The extent of the inaccuracy increases with the number of amino acids in the loop. The loop amino acids' side chains dihedral angles are often approximated from a rotamer library, but can worsen the inaccuracy of side chain packing in the overall model. Andrej Sali's homology modeling suite MODELLER includes a facility explicitly designed for loop modeling by a satisfaction of spatial restraints method. All methods require an upload of the PDB file and some require the specification of the loop location.".
- Loop_modeling wikiPageExternalLink superlooper.
- Loop_modeling wikiPageExternalLink falc-loop.seoklab.org.
- Loop_modeling wikiPageExternalLink modloop.
- Loop_modeling wikiPageExternalLink ~rapper.
- Loop_modeling wikiPageID "8865843".
- Loop_modeling wikiPageLength "9555".
- Loop_modeling wikiPageOutDegree "32".
- Loop_modeling wikiPageRevisionID "671232034".
- Loop_modeling wikiPageWikiLink Adenosine_diphosphate.
- Loop_modeling wikiPageWikiLink Amino_acid.
- Loop_modeling wikiPageWikiLink Andrej_Šali.
- Loop_modeling wikiPageWikiLink Biomolecular_structure.
- Loop_modeling wikiPageWikiLink Breast_cancer.
- Loop_modeling wikiPageWikiLink Category:Bioinformatics.
- Loop_modeling wikiPageWikiLink Category:Protein_methods.
- Loop_modeling wikiPageWikiLink Category:Protein_structure.
- Loop_modeling wikiPageWikiLink Conformational_isomerism.
- Loop_modeling wikiPageWikiLink Conserved_sequence.
- Loop_modeling wikiPageWikiLink De_novo_protein_structure_prediction.
- Loop_modeling wikiPageWikiLink Dihedral_angle.
- Loop_modeling wikiPageWikiLink Electron_density.
- Loop_modeling wikiPageWikiLink Globular_protein.
- Loop_modeling wikiPageWikiLink Homology_modeling.
- Loop_modeling wikiPageWikiLink MODELLER.
- Loop_modeling wikiPageWikiLink Nuclear_magnetic_resonance_spectroscopy_of_proteins.
- Loop_modeling wikiPageWikiLink Peptide_sequence.
- Loop_modeling wikiPageWikiLink Protein.
- Loop_modeling wikiPageWikiLink Protein_Data_Bank_(file_format).
- Loop_modeling wikiPageWikiLink Protein_folding.
- Loop_modeling wikiPageWikiLink Protein_structure_prediction.
- Loop_modeling wikiPageWikiLink Ramachandran_plot.
- Loop_modeling wikiPageWikiLink Sequence_alignment.
- Loop_modeling wikiPageWikiLink Side_chain.
- Loop_modeling wikiPageWikiLink Solvent.
- Loop_modeling wikiPageWikiLink Structural_motif.
- Loop_modeling wikiPageWikiLink Turn_(biochemistry).
- Loop_modeling wikiPageWikiLink X-ray_crystallography.
- Loop_modeling wikiPageWikiLinkText "Loop modeling".
- Loop_modeling wikiPageWikiLinkText "loop modeling".
- Loop_modeling wikiPageUsesTemplate Template:Outdated.
- Loop_modeling wikiPageUsesTemplate Template:Reflist.
- Loop_modeling subject Category:Bioinformatics.
- Loop_modeling subject Category:Protein_methods.
- Loop_modeling subject Category:Protein_structure.
- Loop_modeling hypernym Problem.
- Loop_modeling type Disease.
- Loop_modeling type Biophysic.
- Loop_modeling type Biostatistic.
- Loop_modeling type Method.
- Loop_modeling comment "Loop modeling is a problem in protein structure prediction requiring the prediction of the conformations of loop regions in proteins with or without the use of a structural template. Computer programs that solve these problems have been used to research a broad range of scientific topics from ADP to breast cancer.".
- Loop_modeling label "Loop modeling".
- Loop_modeling sameAs Q6675846.
- Loop_modeling sameAs m.027mjfk.
- Loop_modeling sameAs Q6675846.
- Loop_modeling wasDerivedFrom Loop_modeling?oldid=671232034.
- Loop_modeling isPrimaryTopicOf Loop_modeling.