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 […]
View View   Download Download (PDF)   
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) […]
View View   Download Download (PDF)   
Linchuan Li, Xingjian Li, Guangming Tan, Mingyu Chen, Peiheng Zhang
Heterogeneous architecture is becoming an important way to build a massive parallel computer system, i.e. the CPU-GPU heterogeneous systems ranked in Top500 list. However, it is a challenge to efficiently utilize massive parallelism of both applications and architectures on such heterogeneous systems. In this paper we present a practice on how to exploit and orchestrate […]
Edward W. Lowe Jr., Nils Woetzel, Jens Meiler
Three initial fits of 1ubi in a 6.6A resolution synthesized density map had backbone RMSDs to the correct placement of 2.7, 2.9 and 6.6A. They have been refined with a Powell optimizer [5] in 10 iterations using 6 directions, 3 rotations a, beta with 0.15 radians and gamma with 0.075 radians starting direction to cover […]
Xiaokang Zhang, Xing Zhang, Z. Hong Zhou
Recent advancements in cryo-electron microscopy (cryoEM) have made it technically possible to determine the three-dimensional (3D) structures of macromolecular complexes at atomic resolution. However, processing the large amount of data needed for atomic resolution reconstructions requires either accessing to very expensive computer clusters or waiting for weeks of continuous computation in a personal computer (PC). […]
Hemant D. Tagare, Andrew Barthel, Fred J. Sigworth
Maximum-likelihood (ML) estimation has very desirable properties for reconstructing 3D volumes from noisy cryo-EM images of single macromolecular particles. Current implementations of ML estimation make use of the Expectation-Maximization (EM) algorithm or its variants. However, the EM algorithm is notoriously computation-intensive, as it involves integrals over all orientations and positions for each particle image. We […]

* * *

* * *

Follow us on Twitter

HGPU group

1662 peoples are following HGPU @twitter

Like us on Facebook

HGPU group

337 people like HGPU on Facebook

* * *

Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

The platforms are

Node 1
  • GPU device 0: nVidia GeForce GTX 560 Ti 2GB, 822MHz
  • GPU device 1: AMD/ATI Radeon HD 6970 2GB, 880MHz
  • CPU: AMD Phenom II X6 @ 2.8GHz 1055T
  • RAM: 12GB
  • OS: OpenSUSE 13.1
  • SDK: nVidia CUDA Toolkit 6.5.14, AMD APP SDK 3.0
Node 2
  • GPU device 0: AMD/ATI Radeon HD 7970 3GB, 1000MHz
  • GPU device 1: AMD/ATI Radeon HD 5870 2GB, 850MHz
  • CPU: Intel Core i7-2600 @ 3.4GHz
  • RAM: 16GB
  • OS: OpenSUSE 12.3
  • SDK: AMD APP SDK 3.0

Completed OpenCL project should be uploaded via User dashboard (see instructions and example there), compilation and execution terminal output logs will be provided to the user.

The information send to hgpu.org will be treated according to our Privacy Policy

HGPU group © 2010-2015 hgpu.org

All rights belong to the respective authors

Contact us: