ArticleBMC bioinformatics2014
BioShell-Threading: versatile Monte Carlo package for protein 3D threading.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.Frontiers in molecular biosciences · 2021Review
- Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.Journal of chemical information and modeling · 2020Article
- Prediction of Protein Tertiary Structure via Regularized Template Classification Techniques.Molecules (Basel, Switzerland) · 2020Article
- Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling.Journal of molecular modeling · 2019Article
- EigenTHREADER: analogous protein fold recognition by efficient contact map threading.Bioinformatics (Oxford, England) · 2017Article
- SFESA: a web server for pairwise alignment refinement by secondary structure shifts.BMC bioinformatics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe comparative modeling approach to protein structure prediction inherently relies on a template structure. Before building a model such a template protein has to be found and aligned with the query sequence. Any error made on this stage may dramatically affects the quality of result. There is a need, therefore, to develop accurate and sensitive alignment protocols.
resultsBioShell threading software is a versatile tool for aligning protein structures, protein sequences or sequence profiles and query sequences to a template structures. The software is also capable of sub-optimal alignment generation. It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. The implemented Monte Carlo search engine greatly facilitates the development and benchmarking of new alignment scoring schemes even when the functions exhibit non-deterministic polynomial-time complexity.
conclusionsNumerical experiments indicate that the new threading application offers template detection abilities and provides much better alignments than other methods. The package along with documentation and examples is available at: http://bioshell.pl/threading3d.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.