The Biomolecular Interaction Network Database and related tools 2005 update

Abstract

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machinereadable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. INTRODUCTIONIn light of the vast scientific resources made available through genomics, the science of deciphering molecular mechanisms is expanding rapidly. Scientists who once hunted for disease genes or sought to distinguish key concepts in evolution are now turning their attention to the details of molecular assembly and mechanism to further understand medicine and the key concepts underlying biology. The Biomolecular Interaction Network Database (BIND) was designed to store complete information about molecular assembly through a database structure in order to archive interactions and reactions arising from biopolymers (protein, RNA and DNA), as well as small molecules, lipids and carbohydrates. Detailed information about molecular mechanism, such as the chemical product(s) of an enzymatic reaction, can be encoded in BIND. The underlying ontology of the BIND database is chemistry, and as such, BIND is capable of storing information about molecular interactions to atomic resolution. The taxonomic scope of BIND is

Conservation and topology of protein interaction networks under duplication-divergence evolution

“…S5-S7). This suggests that the available empirical PPI network for yeast (20) has essentially reached its asymptotic degree distribution, for k Յ 20. By contrast, global convergence of the GDD model is typically quite slow for large growth rate regimes with little biological relevance, as shown in SI Appendix, Numerical simulations, Figs.…”

“…Although the GDD model can, in principle, accommodate 1q ϩ 6␥ ij fitting parameters, and any evolutionary variations or fluctuations q (n) and ␥ ij (n) , we have restricted all quantitative comparisons with the empirical data (20) to biologically relevant regimes, limited to one or two effective fitting parameters, only.…”

“…The results, corresponding to 10 3 to 10 4 protein nodes and low network growth rates in the conserved, scale-free regime (1Ͻ M Յ MЈ), are compared with Yeast PPI network data (20) (Fig. 6), both for the connectivity distribution p k and the first-neighbor average connectivity g k (18) (see Fig.…”

Predicting genetic modifier loci using functional gene networks

“…We treated subsets of the WI5 (literature, scaffold, core1, core2, noncore) separately, providing different confidence scores for the different data subsets, rather than a single averaged confidence score across all interactions of the set. The WI5 literature-curated subset was combined with literature-based protein physical interactions from BIND (Alfarano et al 2005), IntAct (Kerrien et al 2007), and MINT (Chatr-aryamontri et al 2007) to construct the literature-curated protein physical interaction set (CE-LC). Genetic interactions (CE-GT) (;2200 interactions among ;1000 genes) were included from Figure 5.…”

A complete small molecule dataset from the protein data bank

“…For our small molecule interaction database (SMID) resource [11], we wanted a high quality, up-to-date dataset of the PDB small molecules. We have combined existing algorithms with some of our own improvements to come up with what we feel is now the most comprehensive, and accurate, set of PDB small molecules.…”