ArticleBMC research notes2011
GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.
Article in BMC research notes, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Predicting the Anti-SARS-CoV-2 Potential of Isoquinoline Alkaloids from Brazilian Siparunaceae Species Using Chemometric Tools.International journal of molecular sciences · 2025Article
- In Silico and In Vitro Studies of Terpenes from the Fabaceae Family Using the Phenotypic Screening Model against the SARS-CoV-2 Virus.Pharmaceutics · 2024Article
- In Silico and In Vitro Evaluation of the Antifungal Activity of a New Chromone Derivative againstBiotech (Basel (Switzerland)) · 2024Article
- A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.Journal of proteomics & bioinformatics · 2016Article
- Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform.Current pharmaceutical design · 2016Review
- Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.PLoS computational biology · 2015Article
- Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.PloS one · 2015Article
- Accelerated protein structure comparison using TM-score-GPU.Bioinformatics (Oxford, England) · 2012Article
- Accelerating large-scale protein structure alignments with graphics processing units.BMC research notes · 2012Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundCalculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH.
findingsThe Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used.
conclusionsGPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale.
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