Literature DB >> 36227540

From Genome Mining to Protein Engineering: A Structural Bioinformatics Route.

Derek J Smith1.   

Abstract

This chapter outlines applications in genome mining, along with computational methods to predict protein structure and protein-ligand docking. It offers a simple computational route to rapidly identify proteins of interest from genomic and proteomic data, to accurately predict their three-dimensional structures, and to dock small molecules to their binding pockets and strategies to improve their biophysical properties depending on the needs of the experimental researcher.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Directed evolution; Genome mining; Protein engineering; Protein structure prediction; Small molecule docking; Structural bioinformatics

Mesh:

Substances:

Year:  2023        PMID: 36227540     DOI: 10.1007/978-1-0716-2617-7_5

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  39 in total

Review 1.  Protein-structure prediction by recombination of fragments.

Authors:  Janusz M Bujnicki
Journal:  Chembiochem       Date:  2006-01       Impact factor: 3.164

2.  Accurate modeling of protein conformation by automatic segment matching.

Authors:  M Levitt
Journal:  J Mol Biol       Date:  1992-07-20       Impact factor: 5.469

3.  Comparative protein modelling by satisfaction of spatial restraints.

Authors:  A Sali; T L Blundell
Journal:  J Mol Biol       Date:  1993-12-05       Impact factor: 5.469

4.  Low-homology protein threading.

Authors:  Jian Peng; Jinbo Xu
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

5.  The emerging role of biosynthetic gene clusters in plant defense and plant interactions.

Authors:  Guy Polturak; Anne Osbourn
Journal:  PLoS Pathog       Date:  2021-07-02       Impact factor: 6.823

6.  An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes.

Authors:  Matthew T Robey; Lindsay K Caesar; Milton T Drott; Nancy P Keller; Neil L Kelleher
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-11       Impact factor: 11.205

7.  antiSMASH 6.0: improving cluster detection and comparison capabilities.

Authors:  Kai Blin; Simon Shaw; Alexander M Kloosterman; Zach Charlop-Powers; Gilles P van Wezel; Marnix H Medema; Tilmann Weber
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

Review 8.  Mining and unearthing hidden biosynthetic potential.

Authors:  Kirstin Scherlach; Christian Hertweck
Journal:  Nat Commun       Date:  2021-06-23       Impact factor: 14.919

9.  Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in Litsea cubeba.

Authors:  Xiao-Jiao Han; Yang-Dong Wang; Yi-Cun Chen; Li-Yuan Lin; Qing-Ke Wu
Journal:  PLoS One       Date:  2013-10-09       Impact factor: 3.240

10.  RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Cole H Christie; Kenneth Dalenberg; Luigi Di Costanzo; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Sai Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranović; Dmytro Guzenko; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Harry Namkoong; Ezra Peisach; Irina Persikova; Chris Randle; Alexander Rose; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Yi-Ping Tao; Maria Voigt; John D Westbrook; Jasmine Y Young; Christine Zardecki; Marina Zhuravleva
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

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