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Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia
The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational Structural Biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades the amount of structural data concerning proteins and other […]
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Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie
BACKGROUND: Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is […]
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Thai V. Hoang, Xavier Cavin, David W. Ritchie
Fitting high resolution protein structures into low resolution cryo-electron microscopy (cryo-EM) density maps is an important technique for modeling the atomic structures of very large macromolecular assemblies. This article presents "gEMfitter", a highly parallel fast Fourier transform (FFT) EM density fitting program which can exploit the special hardware properties of modern graphics processor units (GPUs) […]
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Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman
Small Angle Scattering (SAS) of X-rays or neutrons is an experimental technique that provides valuable structural information for biological macromolecules under physiological conditions and with no limitation on the molecular size. In order to refine molecular structure against experimental SAS data, ab initio prediction of the scattering profile must be recomputed hundreds of thousands of […]
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Marco Maggioni, Tanya Berger-Wolf, Jie Liang
The Chemical Master Equation (CME) is a stochastic and discrete-state continuous-time model for macromolecular reaction networks inside the cell. Under this theoretical framework, the solution of a sparse linear system provides the steady-state probability landscape over the molecular microstates. The CME framework can in fact reveal important insights into basic principles on how biological networks […]
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Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho
Molecular dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. We recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In our present study, we analyze […]
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Matthias Leinweber, Lars Baumgartner, Marco Mernberger, Thomas Fober, Eyke Hullermeier, Gerhard Klebe, Bernd Freisleben
In this paper, we present a novel approach for using a GPU-based Cloud computing infrastructure to efficiently perform a structural comparison of protein binding sites. The original CPU-based Java version of a recent graph-based algorithm called SEGA has been rewritten in OpenCL to run on NVIDIA GPUs in parallel on a set of Amazon EC2 […]
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Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin, Marc Baaden
Ray casting on graphics processing units (GPUs) opens new possibilities for molecular visualization. We describe the implementation and calculation of diverse molecular representations such as licorice, ball-and-stick, space-filling van der Waals spheres, and approximated solvent-accessible surfaces using GPUs. We introduce HyperBalls, an improved ball-and-stick representation replacing tubes, linking the atom spheres by hyperboloids that can […]
Dar-Jen Chang, C. Kimmer, Ming Ouyang
Graphics processing units (GPU) on commodity video cards have evolved into powerful computational devices. The RNA secondary structure arises from the primary structure and a backbone of canonical, Watson-Crick base pairings (A-U, C-G), and to a lesser extent, the G-U pairing. Early computational work by Nussinov formulated the problem of RNA secondary structure prediction as […]
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Jian Zhang, I. McQuillan, FangXiang Wu
Tandem mass spectrometry is a powerful experimental tool used in molecular biology to determine the composition of protein mixtures. In a tandem mass experiment, peptide ion selection algorithms generally select only the most abundant peptide ions for further fragmentation. Because of this, the low-abundance proteins in a sample rarely get identified. A Real-Time Peptide-Spectrum Matching […]
Hongbing Zhu, Heng Xiao, JinGuang Gu
Protein structure prediction (PSP) is the process of searching for the min energy of the protein. While many algorithms have being put forward to predict the structure of protein, the complicated computation make the time cost of the algorithms are significantly expensive. CUDA, the newly developing technology, makes us use Graphic Processing Unit (GPU) that […]
M.N. Osman, R. Abdullah, N. AbdulRashid
Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical […]
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