ArticleBMC bioinformatics2010
Fast and accurate protein substructure searching with simulated annealing and GPUs.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- Bayesian Topology Inference of Regulatory Networks under Partial Observability.Results in control and optimization · 2025Article
- Bayesian Optimization for State and Parameter Estimation of Dynamic Networks with Binary Space.Control Technology and Applications. Control Technology and Applications · 2024Article
- Mining folded proteomes in the era of accurate structure prediction.PLoS computational biology · 2022Article
- Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae.The FEBS journal · 2019Article
- Article
- Graphics processing units in bioinformatics, computational biology and systems biology.Briefings in bioinformatics · 2017Review
- Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA.Journal of molecular modeling · 2014Article
- Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.Nucleic acids research · 2013Article
- Multiple graph regularized protein domain ranking.BMC bioinformatics · 2012Article
- GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening.Molecular diversity · 2012Article
- BetaSearch: a new method for querying β-residue motifs.BMC research notes · 2012Article
- PocketAnnotate: towards site-based function annotation.Nucleic acids research · 2012Article
- Accelerating large-scale protein structure alignments with graphics processing units.BMC research notes · 2012Article
- CFMDS: CUDA-based fast multidimensional scaling for genome-scale data.BMC bioinformatics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSearching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioinformatics. While there are many existing methods for structural similarity searching, faster and more accurate approaches are still required, and few current methods are capable of substructure (motif) searching.
resultsWe developed an improved heuristic for tableau-based protein structure and substructure searching using simulated annealing, that is as fast or faster and comparable in accuracy, with some widely used existing methods. Furthermore, we created a parallel implementation on a modern graphics processing unit (GPU).
conclusionsThe GPU implementation achieves up to 34 times speedup over the CPU implementation of tableau-based structure search with simulated annealing, making it one of the fastest available methods. To the best of our knowledge, this is the first application of a GPU to the protein structural search problem.
Indexed as
Identifiers
What OpenQuestion holds
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.