Literature DB >> 28573590

Stereochemistry and Validation of Macromolecular Structures.

Alexander Wlodawer1.   

Abstract

Macromolecular structure is governed by the strict rules of stereochemistry. Several approaches to the validation of the correctness of the interpretation of crystallographic and NMR data that underlie the models deposited in the PDB are utilized in practice. The stereochemical rules applicable to macromolecular structures are discussed in this chapter. Practical, computer-based methods and tools of verification of how well the models adhere to those established structural principles to assure their quality are summarized.

Entities:  

Keywords:  Bond angles; Bond lengths; Crystal structure; Geometrical criteria; NMR structure; Protein Data Bank (PDB); Quality check; Ramachandran plot

Mesh：

Substances：

Year:  2017        PMID： 28573590      PMCID： PMC5560084          DOI： 10.1007/978-1-4939-7000-1_24

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


  44 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.

Authors:  J D WATSON; F H CRICK
Journal:  Nature       Date:  1953-04-25       Impact factor: 49.962

3.  Stable configurations of polypeptide chains.

Authors:  L PAULING; R B COREY
Journal:  Proc R Soc Lond B Biol Sci       Date:  1953-03-11

4.  WHAT IF: a molecular modeling and drug design program.

Authors:  G Vriend
Journal:  J Mol Graph       Date:  1990-03

5.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

6.  Occurrence and role of cis peptide bonds in protein structures.

Authors:  D E Stewart; A Sarkar; J E Wampler
Journal:  J Mol Biol       Date:  1990-07-05       Impact factor: 5.469

7.  Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Authors: 
Journal:  J Mol Biol       Date:  1998-02-20       Impact factor: 5.469

8.  Phi/psi-chology: Ramachandran revisited.

Authors:  G J Kleywegt; T A Jones
Journal:  Structure       Date:  1996-12-15       Impact factor: 5.006

9.  Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO.

Authors:  T A Jones
Journal:  Methods Enzymol       Date:  1985       Impact factor: 1.600

10.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21
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  11 in total

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3.  Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.

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Journal:  Front Mol Biosci       Date:  2022-04-11

Review 4.  Analysis of the quality of crystallographic data and the limitations of structural models.

Authors:  Valentina Arkhipova; Albert Guskov; Dirk-Jan Slotboom
Journal:  J Gen Physiol       Date:  2017-10-31       Impact factor: 4.086

5.  Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue!

Authors:  Pascal Auffinger; Eric Ennifar; Luigi D'Ascenzo
Journal:  RNA       Date:  2020-12-02       Impact factor: 4.942

6.  CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.

Authors:  Dorothee Liebschner; Pavel V Afonine; Nigel W Moriarty; Billy K Poon; Vincent B Chen; Paul D Adams
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-01-01       Impact factor: 7.652

7.  The computational analyses, molecular dynamics of fatty-acid transport mechanism to the CD36 receptor.

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Journal:  Sci Rep       Date:  2021-12-01       Impact factor: 4.379

8.  Novel Mutations in Putative Nicotinic Acid Phosphoribosyltransferases of Mycobacterium tuberculosis and Their Effect on Protein Thermodynamic Properties.

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Journal:  Polymers (Basel)       Date:  2022-04-18       Impact factor: 4.967

9.  Potential Efficacy of β-Amyrin Targeting Mycobacterial Universal Stress Protein by In Vitro and In Silico Approach.

Authors:  Md Amjad Beg; Obaid Afzal; Md Sayeed Akhtar; Abdulmalik S A Altamimi; Afzal Hussain; Md Ali Imam; Mohammad Naiyaz Ahmad; Sidharth Chopra; Fareeda Athar
Journal:  Molecules       Date:  2022-07-18       Impact factor: 4.927

10.  Multi-Subunit SARS-CoV-2 Vaccine Design Using Evolutionarily Conserved T- and B- Cell Epitopes.

Authors:  Burkitkan Akbay; Syed Hani Abidi; Mahmoud A A Ibrahim; Zhussipbek Mukhatayev; Syed Ali
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