The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
Database searching is a main method for protein identification in shotgun proteomics, and many research efforts are dedicated to improving its effectiveness. However, the efficiency of database searching is facing a serious challenge, due to the ever fast growth of protein and peptide databases resulted from genome translations, enzymatic digestions, and post-translational modifications (PTMs). On...
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 Cluster GPU Instances. This new implementation of SEGA has been...
Liquid chromatography-based tandem mass spectrometry (LC-MS) technique allows for identification and quantification of thousands of proteins in parallel. This technique coupled with a feed-forward artificial neural network provides a technique to analyze and select protein panels for use in multi-biomarker panel discovery applications. In this study, we enhance this technique by utilizing massively...
This article describes a GPU-based high-performance computing method to tackle the protein-DNA docking problem. GPU-specific algorithmic techniques are developed to accelerate a docking algorithm that integrates Monte Carlo simulation and simulated annealing. Experiments show that such improved computation speed accelerates the conformational space sampling of the algorithm and increases the chance...
The "Basic Local Alignment Search Tool'' (BLAST) is arguably the most widely used computational tool in bioinformatics. However, the computational power required for routine BLAST analysis has been outstripping Moore's Law due to the exponential growth in the size of the genomic sequence databases that BLAST searches on. To address the above issue, we propose the design and optimization of the...
The massively parallel computing using graphical processing unit (GPU), which based on tens of thousands of parallel threats within hundreds of GPU's streaming processors, has gained broad popularity and attracted researchers in a wide range of application areas from finance, computer aided engineering, computational fluid dynamics, game physics, numerics, science, medical imaging, life science, and...
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 is mainly used on Graphic processing at...
This paper is a report on the migration of the molecular docking application, “Autodock” to NVIDIA CUDA. Autodock is a Drug Discovery Tool that uses a Genetic Algorithm to find the optimal docking position of a ligand to a protein. Speedup of Autodock greatly benefits the drug discovery process. In this paper, we show how significant speed up of Autodock can be achieved using NVIDIA CUDA. This paper...
Accurate protein loop structure models are important to understand functions of many proteins. One of the main problems in correctly modeling protein loop structures is sampling the large loop backbone conformation space, particularly when the loop is long. In this paper, we present a GPU-accelerated loop backbone structure modeling approach by sampling multiple scoring functions based on pair-wise...
In bioinformatics, alignments are commonly performed in genome and protein sequence analysis for gene identification and evolutionary similarities. There are several approaches for such analysis, each varying in accuracy and computational complexity. Smith-Waterman (SW) is by far the best algorithm for its accuracy in similarity scoring. However, execution time of this algorithm on general purpose...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.