PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 11987160

Automatic annotation of BIND molecular interactions from three-dimensional structures.

J J Salama·I Donaldson·C W Hogue
View original source ↗Export metadata ↓

Abstract

Software to automate the process of extracting molecular interactions from three-dimensional (3D) structures has been developed that records these as Biomolecular Interaction Network Database (BIND) pairwise interaction records. Full annotation of BIND records is provided through a database processing tool called MMDBind, including detailed atom-atom and residue-residue level interaction information. BIND three-dimensional interaction annotation is synthesized by combining information from the Molecular Modeling Database (MMDB), and the HET (heterogen) group dictionary of small molecules in the macromolecular Crystallographic Information Format (mmCIF). Interactions are validated using the Protein Quaternary Structure (PQS) system. A total of 18,166 interactions were removed as being redundant or biologically irrelevant after PQS validation. This first pass MMDBind annotation creates two new divisions of BIND, 3D Biopolymers (BIND-3DBP) comprising 16,737 initial interaction records, and 3D Small Molecules (BIND-3DSM) comprising 48,219 records. Visualization of interacting residues and nucleotides within a macromolecular structure is possible directly from the BIND database owing to added 3D feature annotation within the BIND records that can be conveniently seen using Cn3D ("see-in-3D") after query from the BIND Data Manager. These interaction records provide a further demonstration of the completeness of the BIND data specification and its capabilities as storage and exchange format for all kinds of molecular interactions, including RNA, DNA, protein, and small molecules. Data from the 3DBP and 3DSM sets are available for downloading in Abstract Syntax Notation.1 (ASN.1) or Extensible Markup Language (XML) formats at ftp://ftp.bind.ca/DB/MMDBBind. Data from the 3DBP set is available for interactive query from the BIND Data Manager at www.bind.ca.

Explore related subjects

Crystallography, X-RayDNADatabases as TopicInternetModels, MolecularProtein BindingProtein Structure, QuaternaryRNARibosomesSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

J J Salama, I Donaldson, C W Hogue. Automatic annotation of BIND molecular interactions from three-dimensional structures.. https://doi.org/10.1002/1097-0282(2001%2F2002)61%3A2%3C111%3A%3Aaid-bip10143%3E3.0.co%3B2-8

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2007

Prediction of side-chain conformations on protein surfaces.

An approach is described that improves the prediction of the conformations of surface side chains in crystal structures, given the main-chain conformation of a protein. A key element of the methodology involves the use of the colony energy. This phenomenological term favors conformations found in frequently sampled regions, thereby approximating entropic effects and serving to smooth the potential energy surface. Use of the colony energy significantly improves prediction accuracy for surface side chains with little additional computational cost. Prediction accuracy was quantified as the percentage of side-chain dihedral angles predicted to be within 40 degrees of the angles measured by X-ray diffraction. Use of the colony energy in predictions for single side chains improved the prediction accuracy for chi(1) and chi(1+2) from 65 and 40% to 74 and 59%, respectively. Several other factors that affect prediction of surface side-chain conformations were also analyzed, including the extent of conformational sampling, details of the rotamer library employed, and accounting for the crystallographic environment. The prediction of conformations for polar residues on the surface was generally found to be more difficult than those for hydrophobic residues, except for polar residues participating in hydrogen bonds with other protein groups. For surface residues with hydrogen-bonded side chains, the prediction accuracy of chi(1) and chi(1+2) was 79 and 63%, respectively. For surface polar residues, in general (all side-chain prediction), the accuracy of chi(1) and chi(1+2) was only 73 and 56%, respectively. The most accurate results were obtained using the colony energy and an all-atom description that includes neighboring molecules in the crystal (protein chains and hetero atoms). Here, the accuracy of chi(1) and chi(1+2) predictions for surface side chains was 82 and 73%, respectively. The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 A, with and without consideration of crystal packing effects, respectively.

Crystallography, X-Ray↗
PubMed2007

Double-stranded cycles: toward C84's belt region.

The reactivity of the double-stranded hydrocarbon cycle with two ether bridges (1) toward iodotrimethylsilane (TMSI) was investigated in some detail. The carbon skeleton of cycle 1 resembles the belt region of a C84 fullerene which makes it a potential precursor to the long sought after fully aromatic derivative. Upon exposure to TMSI, cycle 1 undergoes a cascade of reactions which involve different states of iodination/reduction which ultimately lead to the hydrogenated cycle 5a, whose structure was proven by single-crystal X-ray analysis. A deeper insight into mechanistic aspects of this sequence of conversions was gained by performing the reaction under dry and wet conditions, whereby the latter involved both normal and deuterated water. With the help of detailed NMR correlation studies and DFT computations, all important aspects were clarified including an unexpected selective H/D exchange at the naphthalenic moieties.

Crystallography, X-Ray↗