scholarly journals Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis

2017 ◽  
Vol 73 (3) ◽  
pp. 234-239 ◽  
Author(s):  
Jason C. Cole ◽  
Ilenia Giangreco ◽  
Colin R. Groom
Keyword(s):  
Protein Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Paper Briefly ◽  
Ligand Complex ◽  
Protein Structure Refinement ◽  
Metal Organic ◽  
Structural Database

The Cambridge Structural Database (CSD) is the worldwide resource for the dissemination of all published three-dimensional structures of small-molecule organic and metal–organic compounds. This paper briefly describes how this collection of crystal structures can be used en masse in the context of macromolecular crystallography. Examples highlight how the CSD and associated software aid protein–ligand complex validation, and show how the CSD could be further used in the generation of geometrical restraints for protein structure refinement.

scholarly journals Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis. Addendum

2017 ◽  
Vol 73 (12) ◽  
pp. 1029-1029
Author(s):  
Jason C. Cole ◽  
Ilenia Giangreco ◽  
Colin R. Groom
Keyword(s):  
Protein Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Refinement ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Protein Structure Refinement ◽  
Structure Solution ◽  
Structural Database

An addendum to theIntroductionof Coleet al.[(2017),Acta Cryst.D73, 234–239] is made to recognize the work of Bricogne, Smart and others in the development of methods to make use of Cambridge Structural Database data in protein structure solution.

Improved dihedral-angle restraints for protein structure refinement

2003 ◽  
Vol 36 (1) ◽  
pp. 34-42 ◽  
Author(s):  
John P. Priestle
Keyword(s):  
High Resolution ◽  
Crystal Structures ◽  
Dihedral Angle ◽  
Small Molecule ◽  
Structure Refinement ◽  
Protein Structures ◽  
Dihedral Angles ◽  
Effective Number ◽  
Protein Structure Refinement ◽  
Crystal Contacts

Because of the relatively low-resolution diffraction of typical protein crystals, structure refinement is usually carried out employing stereochemical restraints to increase the effective number of observations. Well defined values for bond lengths and angles are available from small-molecule crystal structures. Such values do not exist for dihedral angles because of the concern that the strong crystal contacts in small-molecule crystal structures could distort the dihedral angles. This paper examines the dihedral-angle distributions in ultra-high-resolution protein structures (1.2 Å or better) as a means of analysing the population frequencies of dihedral angles in proteins and compares these with the stereochemical restraints currently used in one of the more widely used molecular-dynamics refinement packages,X-PLOR, and its successor,CNS. Discrepancies between the restraints used in these programs and what is actually seen in high-resolution protein structures are examined and an improved set of dihedral-angle restraint parameters are derived from these inspections.

scholarly journals A branch and bound algorithm for protein structure refinement from sparse NMR data sets 1 1Edited by F. Cohen

1999 ◽  
Vol 285 (4) ◽  
pp. 1691-1710 ◽  
Author(s):  
Daron M. Standley ◽  
Volker A. Eyrich ◽  
Anthony K. Felts ◽  
Richard A. Friesner ◽  
Ann E. McDermott
Keyword(s):  
Protein Structure ◽  
Branch And Bound ◽  
Structure Refinement ◽  
Branch And Bound Algorithm ◽  
Data Sets ◽  
Protein Structure Refinement ◽  
Nmr Data

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

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