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Protein model quality assessment
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Ebook "Computational modelling of the human islet amyloid polypeptide" offers readers a comprehensive introduction to amyloid proteins and the computational methods used with them. Katrine Skeby critically assesses and compares both the literature and the experiments performed by other researchers, which further elevates the quality and relevance of her own work.
132p
tudohanhtau1006
29-03-2024
5
1
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As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques.
12p
viwyoming2711
16-12-2020
11
1
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Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR), a common method to solve the phase problem faced by macromolecular crystallography. The success of MR depends on the accuracy of a search model. Unfortunately, this parameter remains unknown until the final structure of the target protein is determined.
12p
viwyoming2711
16-12-2020
10
0
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Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality of a single protein model, which is important for selecting a few good models out of a large model pool consisting of mostly low-quality models, is still a largely unsolved problem.
9p
vioklahoma2711
19-11-2020
6
0
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Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of experimentally resolved structures, and databases such as the Protein Data Bank, also implies large scale structural similarity analyses to retrieve and classify macromolecular data.
8p
vioklahoma2711
19-11-2020
8
0
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Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicted protein models in perspective is one of the key components of successful protein structure prediction.
8p
viflorida2711
30-10-2020
10
1
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Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi -Cαi+1 (θ) and the rotational angle about the Cαi -Cαi+1 bond (τ). Thus, their accurate prediction is useful for structure prediction and model refinement.
8p
viconnecticut2711
28-10-2020
8
0
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The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as decoy discrimination. However, these two aspects are found to be mutually exclusive in many statistical potentials.
11p
vijisoo2711
27-10-2020
20
0
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Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to determine a model’s utility and potential applications.
10p
vicolorado2711
22-10-2020
11
0
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