Literature DB >> 16808918

A normalised scale for structural genomics target ranking: the OB-Score.

Ian M Overton1, Geoffrey J Barton.   

Abstract

Target selection and ranking is fundamental to structural genomics. We present a Z-score scale, the "OB-Score", to rank potential targets by their predicted propensity to produce diffraction-quality crystals. The OB-Score is derived from a matrix of predicted isoelectric point and hydrophobicity values for nonredundant PDB entries solved to <or=3.0 A against a background of UniRef50. A highly significant difference was found between the OB-Scores for TargetDB test datasets. A wide range of OB-Scores was observed across 241 proteomes and within 7868 PfamA families; 73.4% of PfamA families contain >or=1 member with a high OB-Score, presenting favourable candidates for structural studies.

Mesh:

Substances:

Year:  2006        PMID: 16808918     DOI: 10.1016/j.febslet.2006.06.015

Source DB:  PubMed          Journal:  FEBS Lett        ISSN: 0014-5793            Impact factor:   4.124


  27 in total

1.  Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.

Authors:  James E Bray
Journal:  J Struct Funct Genomics       Date:  2012-02-22

2.  Predicting protein crystallization propensity from protein sequence.

Authors:  György Babnigg; Andrzej Joachimiak
Journal:  J Struct Funct Genomics       Date:  2010-02-23

3.  The challenge of protein structure determination--lessons from structural genomics.

Authors:  Lukasz Slabinski; Lukasz Jaroszewski; Ana P C Rodrigues; Leszek Rychlewski; Ian A Wilson; Scott A Lesley; Adam Godzik
Journal:  Protein Sci       Date:  2007-11       Impact factor: 6.725

Review 4.  High-throughput protein purification and quality assessment for crystallization.

Authors:  Youngchang Kim; Gyorgy Babnigg; Robert Jedrzejczak; William H Eschenfeldt; Hui Li; Natalia Maltseva; Catherine Hatzos-Skintges; Minyi Gu; Magdalena Makowska-Grzyska; Ruiying Wu; Hao An; Gekleng Chhor; Andrzej Joachimiak
Journal:  Methods       Date:  2011-08-31       Impact factor: 3.608

Review 5.  Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.

Authors:  Huilin Wang; Liubin Feng; Geoffrey I Webb; Lukasz Kurgan; Jiangning Song; Donghai Lin
Journal:  Brief Bioinform       Date:  2018-09-28       Impact factor: 11.622

6.  Sequence-Based Prediction of Transmembrane Protein Crystallization Propensity.

Authors:  Qizhi Zhu; Lihua Wang; Ruyu Dai; Wei Zhang; Wending Tang; Yannan Bin; Zeliang Wang; Junfeng Xia
Journal:  Interdiscip Sci       Date:  2021-06-18       Impact factor: 2.233

7.  Physico-chemical determinants of soluble intrabody expression in mammalian cell cytoplasm.

Authors:  Erik Kvam; Michael R Sierks; Charles B Shoemaker; Anne Messer
Journal:  Protein Eng Des Sel       Date:  2010-04-08       Impact factor: 1.650

8.  Understanding the physical properties that control protein crystallization by analysis of large-scale experimental data.

Authors:  W Nicholson Price; Yang Chen; Samuel K Handelman; Helen Neely; Philip Manor; Richard Karlin; Rajesh Nair; Jinfeng Liu; Michael Baran; John Everett; Saichiu N Tong; Farhad Forouhar; Swarup S Swaminathan; Thomas Acton; Rong Xiao; Joseph R Luft; Angela Lauricella; George T DeTitta; Burkhard Rost; Gaetano T Montelione; John F Hunt
Journal:  Nat Biotechnol       Date:  2009-01       Impact factor: 54.908

9.  The Scottish Structural Proteomics Facility: targets, methods and outputs.

Authors:  Muse Oke; Lester G Carter; Kenneth A Johnson; Huanting Liu; Stephen A McMahon; Xuan Yan; Melina Kerou; Nadine D Weikart; Nadia Kadi; Md Arif Sheikh; Stefan Schmelz; Mark Dorward; Michal Zawadzki; Christopher Cozens; Helen Falconer; Helen Powers; Ian M Overton; C A Johannes van Niekerk; Xu Peng; Prakash Patel; Roger A Garrett; David Prangishvili; Catherine H Botting; Peter J Coote; David T F Dryden; Geoffrey J Barton; Ulrich Schwarz-Linek; Gregory L Challis; Garry L Taylor; Malcolm F White; James H Naismith
Journal:  J Struct Funct Genomics       Date:  2010-04-24

Review 10.  Computational crystallization.

Authors:  Irem Altan; Patrick Charbonneau; Edward H Snell
Journal:  Arch Biochem Biophys       Date:  2016-01-11       Impact factor: 4.013

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.