ArticleComparative and functional genomics2003
Ab initio protein structure prediction using pathway models.
Article in Comparative and functional genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed.
- AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants.Viruses · 2024Article
- Before and after AlphaFold2: An overview of protein structure prediction.Frontiers in bioinformatics · 2023Review
- Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation.Biophysical chemistry · 2021Article
- Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.Biochimica et biophysica acta · 2012Article
- Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models.BMC structural biology · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ab initio prediction is the challenging attempt to predict protein structures based only on sequence information and without using templates. It is often divided into two distinct sub-problems: (a) the scoring function that can distinguish native, or native-like structures, from non-native ones; and (b) the method of searching the conformational space. Currently, there is no reliable scoring function that can always drive a search to the native fold, and there is no general search method that can guarantee a significant sampling of near-natives. Pathway models combine the scoring function and the search. In this short review, we explore some of the ways pathway models are used in folding, in published works since 2001, and present a new pathway model, HMMSTR-CM, that uses a fragment library and a set of nucleation/propagation-based rules. The new method was used for ab initio predictions as part of CASP5. This work was presented at the Winter School in Bioinformatics, Bologna, Italy, 10-14 February 2003.
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Registered trials
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