Literature DB >> 15629199

The advantages and limitations of protein crystal structures.

K Ravi Acharya1, Matthew D Lloyd.   

Abstract

Crystal structure analysis using X-ray diffraction is, in many cases, the most advanced method available for obtaining high-resolution structural information about biological macromolecules. The ways in which X-ray diffraction data are collected and refined have a strong impact on the final quality of the structural models and the type and magnitude of their associated errors. It is becoming increasingly necessary for both structural and non-structural biologists to judge the reliability and accuracy of these models, which are being used in many aspects of research, including structure-based drug design, and to address detailed functional biological questions. In this article, we discuss how errors in these models arise and how they can be evaluated, and we argue for even more stringent validation checks and documentation of structures before deposition with the Protein Data Bank.

Mesh:

Year:  2005        PMID: 15629199     DOI: 10.1016/j.tips.2004.10.011

Source DB:  PubMed          Journal:  Trends Pharmacol Sci        ISSN: 0165-6147            Impact factor:   14.819


  37 in total

1.  Virtual screening using a conformationally flexible target protein: models for ligand binding to p38α MAPK.

Authors:  Natalie B Vinh; Jamie S Simpson; Peter J Scammells; David K Chalmers
Journal:  J Comput Aided Mol Des       Date:  2012-04-20       Impact factor: 3.686

2.  Use of Multiple Ion Fragmentation Methods to Identify Protein Cross-Links and Facilitate Comparison of Data Interpretation Algorithms.

Authors:  Bingqing Zhao; Colin P Reilly; Caroline Davis; Andreas Matouschek; James P Reilly
Journal:  J Proteome Res       Date:  2020-06-04       Impact factor: 4.466

3.  Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity.

Authors:  Peng Zhou; Congcong Wang; Feifei Tian; Yanrong Ren; Chao Yang; Jian Huang
Journal:  J Comput Aided Mol Des       Date:  2013-01-10       Impact factor: 3.686

4.  Combining ion mobility spectrometry with hydrogen-deuterium exchange and top-down MS for peptide ion structure analysis.

Authors:  Mahdiar Khakinejad; Samaneh Ghassabi Kondalaji; Hossein Maleki; James R Arndt; Gregory C Donohoe; Stephen J Valentine
Journal:  J Am Soc Mass Spectrom       Date:  2014-09-30       Impact factor: 3.109

5.  Orthogonal Mass Spectrometry-Based Footprinting for Epitope Mapping and Structural Characterization: The IL-6 Receptor upon Binding of Protein Therapeutics.

Authors:  Ke Sherry Li; Guodong Chen; Jingjie Mo; Richard Y-C Huang; Ekaterina G Deyanova; Brett R Beno; Steve R O'Neil; Adrienne A Tymiak; Michael L Gross
Journal:  Anal Chem       Date:  2017-07-06       Impact factor: 6.986

6.  Opposites Attract: Escherichia coli Heptosyltransferase I Conformational Changes Induced by Interactions between the Substrate and Positively Charged Residues.

Authors:  Joy M Cote; Cody J S Hecht; Kaelan R Patel; Carlos A Ramirez-Mondragon; Yuk Y Sham; Erika A Taylor
Journal:  Biochemistry       Date:  2020-02-10       Impact factor: 3.162

7.  Conformational Differences Are Observed for the Active and Inactive Forms of Pinholin S21 Using DEER Spectroscopy.

Authors:  Tanbir Ahammad; Daniel L Drew; Indra D Sahu; Rasal H Khan; Brandon J Butcher; Rachel A Serafin; Alberto P Galende; Robert M McCarrick; Gary A Lorigan
Journal:  J Phys Chem B       Date:  2020-12-08       Impact factor: 2.991

8.  Structural Dynamics and Topology of the Inactive Form of S21 Holin in a Lipid Bilayer Using Continuous-Wave Electron Paramagnetic Resonance Spectroscopy.

Authors:  Tanbir Ahammad; Daniel L Drew; Rasal H Khan; Indra D Sahu; Emily Faul; Tianyan Li; Gary A Lorigan
Journal:  J Phys Chem B       Date:  2020-06-19       Impact factor: 2.991

9.  Probing the active center of benzaldehyde lyase with substitutions and the pseudosubstrate analogue benzoylphosphonic acid methyl ester.

Authors:  Gabriel S Brandt; Natalia Nemeria; Sumit Chakraborty; Michael J McLeish; Alejandra Yep; George L Kenyon; Gregory A Petsko; Frank Jordan; Dagmar Ringe
Journal:  Biochemistry       Date:  2008-06-21       Impact factor: 3.162

Review 10.  Use of electron paramagnetic resonance to solve biochemical problems.

Authors:  Indra D Sahu; Robert M McCarrick; Gary A Lorigan
Journal:  Biochemistry       Date:  2013-08-20       Impact factor: 3.162

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