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Hokkaido University Collection of Scholarly and Academic Papers >
Graduate School of Life Science / Faculty of Advanced Life Science >
Peer-reviewed Journal Articles, etc >
LAFIRE : software for automating the refinement process of protein-structure analysis
| Title: | LAFIRE : software for automating the refinement process of protein-structure analysis |
| Authors: | Yao, Min Browse this author →KAKEN DB | | Zhou, Yong Browse this author | | Tanaka, Isao Browse this author →KAKEN DB |
| Keywords: | automatic refinement | | structural genomics | | high-throughput structure analysis |
| Issue Date: | 2006 |
| Publisher: | International Union of Crystallography |
| Journal Title: | Acta Crystallographica Section D Biological Crystallography |
| Volume: | 62 |
| Issue: | 2 |
| Start Page: | 189 |
| End Page: | 196 |
| Publisher DOI: | 10.1107/S0907444905038965 |
| PMID: | 16421450 |
| Abstract: | Manual intervention is usually required in the multiple rounds of refinement of protein crystal structures, including linking and/or extending the fragments of the initial model and rebuilding (fitting) ill-matched residues using computer-graphics software. Such manual modification is both time-consuming and requires a great deal of expertise in crystallography. Consequently, the refinement process becomes the bottleneck for high-throughput structure analysis. A program, Local correlation coefficient-based Automatic FItting for REfinement (LAFIRE), has been developed to achieve manual intervention-free refinement. This program was designed to perform the entire process of protein structural refinement automatically using the refinement programs CNS1.1 (CNS v.1.1) or REFMAC5. The automatic process begins from an initial model, which can be approximate, fragmentary or even only main-chain, and refines it to the final model including water molecules, controlled by monitoring the Rfree factor. More than 30 structures have now been refined successfully in a fully or semi-automatic manner within a few hours or days using LAFIRE. |
| Relation: | http://journals.iucr.org/ |
| Type: | article |
| URI: | http://hdl.handle.net/2115/14916 |
| Appears in Collections: | 生命科学院・先端生命科学研究院 (Graduate School of Life Science / Faculty of Advanced Life Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 姚 閔
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