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.

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 The development and use of a crystallographic database

2016 ◽  
Vol 72 (2) ◽  
pp. 167-168 ◽  
Author(s):  
Carl Henrik Görbitz
Keyword(s):  
Crystal Structures ◽  
Small Molecule ◽  
Organometallic Compounds ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Individual Crystal ◽  
Data Source ◽  
Structural Database

To scientists working with small-molecule or organometallic compounds, the Cambridge Structural Database constitutes an extremely important tool for reference to individual crystal structures and as a data source for statistical investigations. The article by Groomet al.[(2016),Acta Cryst.B72, 171–179] provides updated information on the use, development and future of this database.

scholarly journals The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

2017 ◽  
Vol 73 (3) ◽  
pp. 240-245 ◽  
Author(s):  
Colin R. Groom ◽  
Jason C. Cole
Keyword(s):  
Drug Discovery ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structural Chemistry ◽  
Cambridge Structural Database ◽  
Complement Protein ◽  
Ligand Discovery ◽  
Structural Database ◽  
Core Part

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.

The Cambridge Structural Database: a quarter of a million crystal structures and rising

2002 ◽  
Vol 58 (3) ◽  
pp. 380-388 ◽  
Author(s):  
Frank H. Allen
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Small Molecule ◽  
Structure Data ◽  
Crystal Structure Data ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
Chemical Information ◽  
Structural Database ◽  
Statistical Survey

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500000 crystal structures by the year 2010.

First global analysis of the GSK database of small molecule crystal structures

CrystEngComm ◽  
2021 ◽  
Author(s):  
Leen N. Kalash ◽  
Jason C. Cole ◽  
Royston C. B. Copley ◽  
Colin M. Edge ◽  
Alexandru A. Moldovan ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Small Molecule ◽  
Global Analysis ◽  
Structural Features ◽  
Cambridge Structural Database ◽  
Structure Database ◽  
Structural Database ◽  
Crystal Structure Database

Analysis of the molecular and structural features of the GSK crystal structure database and Cambridge Structural Database leads to improved reliability in hydrogen bond propensity models for pharmaceutical polymorphs.

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.

A list of organometallic kryptoracemates

2015 ◽  
Vol 71 (3) ◽  
pp. 216-221 ◽  
Author(s):  
Ivan Bernal ◽  
Steven Watkins
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Room Temperature ◽  
Cambridge Structural Database ◽  
Acta Cryst ◽  
Influence Of Temperature ◽  
Space Groups ◽  
Chiral Compounds ◽  
Structural Database ◽  
Racemic Crystals

The vast majority of racemic solutions of chiral compounds apparently crystallize at room temperature in non-Sohncke space groups as racemic crystals. However, kryptoracemic crystals composed of nearly enantiomeric pairs occasionally crystallize at room temperature, or appear as low-temperature phases, in Sohncke space groups. As a complement to the previously published catalog of organic kryptoracemates [Fábián & Brock (2010).Acta Cryst.B66, 94–103], 1412 chiral organometallic crystal structures have now been extracted from the Cambridge Structural Database and analyzed. 26 are listed herein as credible kryptoracemates. The possible influence of temperature is discussed, together with some problems in characterizing and classifying these structures.

Utilizing organic and organometallic structural data in powder diffraction

2014 ◽  
Vol 29 (S2) ◽  
pp. S19-S30 ◽  
Author(s):  
Jason C. Cole ◽  
Elena A. Kabova ◽  
Kenneth Shankland
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
Powder Diffraction Data ◽  
Racemic Form ◽  
Structure Solution ◽  
Structural Database

The Cambridge Structural Database (CSD) is a database of small molecule organic and organometallic crystal structures elucidated using X-Ray and neutron crystallography. The CSD is distributed alongside a system of software (the Cambridge Structural Database System) to academic and industrial users. The system contains a number of applications (in particular DASH, ConQuest, and Mogul) that can be used to aid crystallographers in the solution and refinement of crystal structures from powder diffraction data, and in the interpretation of crystal structure models (in particular, Mercury). This publication uses a racemic form of ornidazole (Z′ = 3) to illustrate the efficacy of DASH in the crystal structure solution from powder diffraction data. Furthermore, numerous features in Mogul and Mercury that aid crystal structure solution and interpretation of crystallographic data are revised. Finally, a review of a new method for using database-derived geometric information directly in structural solution is presented.

Oscail, a program package for small-molecule single-crystal crystallography with crystal morphology prediction and molecular modelling

2017 ◽  
Vol 50 (1) ◽  
pp. 320-326 ◽  
Author(s):  
Patrick McArdle
Keyword(s):  
Small Molecule ◽  
Molecular Modelling ◽  
Density Functional ◽  
Crystal Morphology ◽  
Structure Refinement ◽  
Halogen Bonding ◽  
Quantum Calculations ◽  
Functional Theory ◽  
Structure Solution ◽  
Structural Database

Oscail is a program for small-molecule crystallography which includes crystal morphology prediction and an interface to molecular modelling. The Oscail graphical user interface can drive SHELX and Superflip for structure solution and SHELXL for structure refinement. The lattice analysis includes hydrogen bonding, halogen bonding and van der Waals contact stacking. Other facilities include interactive bar charts of space-group frequencies in the Cambridge Structural Database, powder diffraction pattern calculation and reduced cell cluster analysis of structures. The graphics output includes thermal ellipsoid plots and rendered OpenGL and Raster3D photorealism in stills and movies. The molecular modelling includes quantum calculations (MOPAC, extended Hückel and density functional theory) and TINKER molecular mechanics.

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