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Literature DB >> 16940322

Bio3d: an R package for the comparative analysis of protein structures.

Barry J Grant¹, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves.

Abstract

UNLABELLED: An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data. AVAILABILITY: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/

Mesh：

Substances：
Proteins

Year: 2006 PMID： 16940322 DOI： 10.1093/bioinformatics/btl461

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

Keyword Cloud
Cited

480 in total

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2. Abstractions, algorithms and data structures for structural bioinformatics in PyCogent.

Authors: Marcin Cieślik; Zygmunt S Derewenda; Cameron Mura
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3. Conservation of complex knotting and slipknotting patterns in proteins.

Authors: Joanna I Sułkowska; Eric J Rawdon; Kenneth C Millett; Jose N Onuchic; Andrzej Stasiak
Journal: Proc Natl Acad Sci U S A Date: 2012-06-08 Impact factor: 11.205

4. Design and synthesis of Hsp90 inhibitors: exploring the SAR of Sansalvamide A derivatives.

Authors: Robert P Sellers; Leslie D Alexander; Victoria A Johnson; Chun-Chieh Lin; Jeremiah Savage; Ricardo Corral; Jason Moss; Tim S Slugocki; Erinprit K Singh; Melinda R Davis; Suchitra Ravula; Jamie E Spicer; Jenna L Oelrich; Andrea Thornquist; Chung-Mao Pan; Shelli R McAlpine
Journal: Bioorg Med Chem Date: 2010-07-22 Impact factor: 3.641

5. Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel.

Authors: Young-Tae Lee; Edith C Glazer; Richard F Wilson; C David Stout; David B Goodin
Journal: Biochemistry Date: 2011-01-11 Impact factor: 3.162

6. Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function.

Authors: Agnieszka A Kaczor; Ramon Guixà-González; Pau Carrió; Cristian Obiol-Pardo; Manuel Pastor; Jana Selent
Journal: J Mol Model Date: 2012-05-29 Impact factor: 1.810

Bio3d: an R package for the comparative analysis of protein structures.

1. Deconstructing honeybee vitellogenin: novel 40 kDa fragment assigned to its N terminus.

2. Abstractions, algorithms and data structures for structural bioinformatics in PyCogent.

3. Conservation of complex knotting and slipknotting patterns in proteins.

4. Design and synthesis of Hsp90 inhibitors: exploring the SAR of Sansalvamide A derivatives.

5. Three clusters of conformational states in p450cam reveal a multistep pathway for closing of the substrate access channel.

6. Fractal dimension as a measure of surface roughness of G protein-coupled receptors: implications for structure and function.

7. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

8. Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations.

9. Compensatory epistasis explored by molecular dynamics simulations.

10. Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family.