Titlebook: Homology Modeling; Methods and Protocol S?awomir Filipek Book 2023 Springer Science+Business Media, LLC, part of Springer Nature 2023 Prote

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,Illuminating the “Twilight Zone”: Advances in Difficult Protein Modeling,ality only when templates with appreciable sequence identity with a target could be found. The threshold value was long assumed to be around 20–30%. Below this level, obtained sequence identity was getting dangerously close to values that can be obtained by chance, after aligning any random, unrelat

Living-Will

Contact-Assisted Threading in Low-Homology Protein Modeling,cent past. The progress is propelled by the improved accuracy of deep learning-based inter-residue contact map predictors coupled with the rising growth of protein sequence databases. Contact map encodes interatomic interaction information that can be exploited for highly accurate prediction of prot

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Omics and Remote Homology Integration to Decipher Protein Functionality, in the scientific field. Despite each omics possess their own laboratorial protocols, they share a background of bioinformatic tools for data integration and analysis. A recent subset of bioinformatic tools, based on available templates or remote homology protocols, allow computational fast and hig

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Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates,entity and available high-resolution structures. This technique is based on the idea that protein structure shows fewer changes than sequence through evolution. While in this scenario single mutations would minimally perturb the structure, experimental evidence shows otherwise: proteins with high co

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Quality Estimates for 3D Protein Models,ture prediction field has been how to estimate the accuracy of the predicted 3D models, on both a local and global level, in the absence of known structures. We must be able to accurately measure the confidence that we have in the quality predicted 3D models of proteins for them to become widely ado

Ankylo-

Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategyd irregular hydrogen bonding patterns. Refinement approaches based on molecular dynamics (MD) simulations using different types of restraints have performed well since CASP10. ReFOLD, developed by the McGuffin group, was one of the many MD-based refinement approaches, which were tested in CASP 12. W

Irascible

Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling,a Bank. Because of this disparity, methods for modeling membrane proteins are fewer and of lower quality than those for modeling soluble proteins. However, better expression, crystallization, and cryo-EM techniques have prompted a recent increase in experimental structures of membrane proteins, whic

清洗

Homology Modeling of the G Protein-Coupled Receptors,able for GPCRs, homology modeling remains a relevant method for studying these receptors and for discovering new ligands for them. Here we describe the state-of-the-art methods for modeling GPCRs, starting from template selection, through fine-tuning sequence alignment to model refinement.

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