The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described.

AVAILABILITY AND IMPLEMENTATION

The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and can be accessed from http://wwpdb.org.

CONTACT

jwest@rcsb.rutgers.edu.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

From Mesoscale Back to Atomistic Models: A Fast Reverse-Mapping Procedure for Vinyl Polymer Chains

This paper introduces a systematic procedure to obtain well-relaxed atomistic melt structures from mesocale models of vinyl polymers based on sequences of diads. Following the methodology introduced by Milano and Müller-Plathe [J. Phys. Chem. B. 2005, 109, 18609], coarse-grain models consisting of sequences of superatoms of two different types meso and racemo have been used to relax mesocale melts of atactic and syndiotactic polystyrene. The proposed method, based on a fully geometrical approach, does not involve expensive potential energy and force evaluations and allows a very fast and efficient reconstruction of the atomistic detail. The method, successfully tested against experimental data, allows us to obtain all atom models of both stereoregular and stereoirregular polymers and opens the possibility of relaxing large molecular weight melts of vinyl chains.

Conformational studies on polypeptide models of collagen. Poly(Gly-Pro-Val), poly(Gly-Pro-Met), poly(Gly-Val-Pro) and poly(Gly-Met-Pro)

The title polytripeptides were synthesized and studied experimentally, by circular dichroism, and theoretically, by quantum mechanical methods. With the exception of poly(Gly-Pro-Val), which was found to be essentially structureless in solution, the other polymers adopt folded conformations, most probably of type II beta-bends. Conclusions from theoretical studies were generally in agreement with the experimental results. In particular, it is noteworthy that the optimized (phi, psi) maps for poly(Gly-Pro-Met) showed the absolute minimum (phi = 60 degree, psi = 0 degrees) located inside the beta II bend space.