MrGrid: A Portable Grid Based Molecular Replacement Pipeline

By Jason W. Schmidberger, Mark A. Bate, Cyril F. Reboul, S. Androulakis, J. Phan, James C. Whisstock, W. Goscinski, David Abramson, Ashley M. Buckle. 2010

5 citations recorded by the source corpus.

Background The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. Methodology/Principal Findings MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. Conclusions MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success.

Subfields: Computer Networks and Communications, Materials Chemistry, Molecular Biology

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In Computer Networks and Communications

1. Yang Zhang

In Materials Chemistry

1. Yan Wang
2. Zhidong Xue
3. Jouko Virtanen
4. Yang Zhang
5. Jianyi Yang
6. Robin Pearce
7. Chengxin Zhang
8. Sitao Wu

In Molecular Biology

1. Yan Wang
2. Zhidong Xue
3. Jouko Virtanen
4. Yang Zhang
5. Jianyi Yang
6. Robin Pearce
7. Chengxin Zhang
8. Ambrish Roy

Citations in the corpus

• I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation (2017, background): “developed MrGrid, a portable grid based MR pipeline that allows multiple MR calculations across a grid of networked computers (7).”