Cargando…

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

BACKGROUND: Calculation 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 suita...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hung, Ling-Hong, Guerquin, Michal, Samudrala, Ram
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Technical Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087690/ https://www.ncbi.nlm.nih.gov/pubmed/21453553 http://dx.doi.org/10.1186/1756-0500-4-97

Ejemplares similares

spyrmsd: symmetry-corrected RMSD calculations in Python
por: Meli, Rocco, et al.
Publicado: (2020)

DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
por: Bell, Eric W., et al.
Publicado: (2019)

Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation
por: Maruyama, Yutaka, et al.
Publicado: (2023)

Ultra-Fast Image Reconstruction of Tomosynthesis Mammography Using GPU
por: Arefan, D., et al.
Publicado: (2015)

Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test
por: Al-jouie, Abdulrhman, et al.
Publicado: (2015)

Weighted Mean Squared Deviation Feature Screening for Binary Features
por: Wang, Gaizhen, et al.
Publicado: (2020)

CARON – Average RMSD of NMR structure ensembles
por: Sikic, Kresimir, et al.
Publicado: (2009)

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations
por: Schreiner, Wolfgang, et al.
Publicado: (2012)

The difficulty of protein structure alignment under the RMSD
por: Li, Shuai Cheng
Publicado: (2013)

A simple calculation method for determination of equivalent square field
por: Shafiei, Seyed Ali, et al.
Publicado: (2012)

Using least median of squares for structural superposition of flexible proteins
por: Liu, Yu-Shen, et al.
Publicado: (2009)

Transformations of superpositions by means of incoherent operations
por: Losada, Marcelo, et al.
Publicado: (2020)

Accelerated protein structure comparison using TM-score-GPU
por: Hung, Ling-Hong, et al.
Publicado: (2012)

T-RMSD: a web server for automated fine-grained protein structural classification
por: Magis, Cedrik, et al.
Publicado: (2013)

The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix
por: Kim, Hyoungrae, et al.
Publicado: (2017)

What Does It “Mean”? A Review of Interpreting and Calculating Different Types of Means and Standard Deviations
por: Martinez, Marilyn N., et al.
Publicado: (2017)

Novel Technique for Growth Plate Analysis Based on the Superposition of T(1)- and T(2)-weighted MR Imaging of Adolescent Wrists
por: Obuchowicz, Rafał, et al.
Publicado: (2019)

Improving the accuracy of template-based predictions by mixing and matching between initial models
por: Liu, Tianyun, et al.
Publicado: (2008)

Fast determination of the optimal rotational matrix for macromolecular superpositions
por: Liu, Pu, et al.
Publicado: (2010)

A fast GPU‐accelerated Monte Carlo engine for calculation of MLC‐collimated electron fields
por: Brost, Eric E., et al.
Publicado: (2022)

GPrimer: a fast GPU-based pipeline for primer design for qPCR experiments
por: Bae, Jeongmin, et al.
Publicado: (2021)

DOPA: GPU-based protein alignment using database and memory access optimizations
por: Hasan, Laiq, et al.
Publicado: (2011)

Essentially exact ground-state calculations by superpositions of nonorthogonal Slater determinants
por: Goto, Hidekazu, et al.
Publicado: (2013)

Performance Evaluation of Algorithms in Lung IMRT: A comparison of Monte Carlo, Pencil Beam, Superposition, Fast Superposition and Convolution Algorithms
por: Verma, T., et al.
Publicado: (2016)

SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
por: Wiewiórka, Marek, et al.
Publicado: (2019)

Protinfo PPC: A web server for atomic level prediction of protein complexes
por: Kittichotirat, Weerayuth, et al.
Publicado: (2009)

fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
por: O’Halloran, Damien M.
Publicado: (2017)

Point Dose Measurement for Verification of Treatment Planning System using an Indigenous Heterogeneous Pelvis Phantom for Clarkson, Convolution, Superposition, and Fast Superposition Algorithms
por: Singh, S., et al.
Publicado: (2019)

Experimental Study on Damage Detection in Timber Specimens Based on an Electromechanical Impedance Technique and RMSD-Based Mahalanobis Distance
por: Wang, Dansheng, et al.
Publicado: (2016)

Standard deviation and standard error of the mean
por: Lee, Dong Kyu, et al.
Publicado: (2015)

Fast 3D dosimetric verifications based on an electronic portal imaging device using a GPU calculation engine
por: Zhu, Jinhan, et al.
Publicado: (2015)

A Novel GPU-based Fast Monte Carlo Photon Dose Calculating Method for Accurate Radiotherapy Treatment Planning
por: M., Karbalaee, et al.
Publicado: (2020)

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores
por: Chikkagoudar, Satish, et al.
Publicado: (2011)

wenda_gpu: fast domain adaptation for genomic data
por: Hippen, Ariel A, et al.
Publicado: (2022)

Superposition of artificial experimental error onto calculated time series: Construction of in-silico data sets
por: Heynderickx, Philippe M., et al.
Publicado: (2018)

Study of nuclear moments and mean square charge radii by collinear fast-beam laser spectrosccopy
por: CERN. Geneva. Proton Synchrotron and Synchrocyclotron Committee
Publicado: (1987)

Hardt condition for superposition of separatrices
por: Pullia, M
Publicado: (1996)

Decoherence rate of mass superpositions
por: Stodolsky, L
Publicado: (1996)

Superposition and interaction: coherence in physics
por: Schlegel, Richard
Publicado: (1980)

Superposition, entanglement and quantum computation
por: Forcer, T M, et al.
Publicado: (2002)

Cannot write session to /tmp/vufind_sessions/sess_b8eqoiriipvn8g1e40bbol76qc