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Three-dimensional pharmacophore methods in drug discovery.
This paper presents a meta-analyses of Cheminformatics Software and its Applications for BioMedical Research, aiming at determining the “building blocks” of peptide-based drug discovery and development. Expand
The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase
Data support a model in which RbpA plays a key role in the σ cycle in actinobacteria, including Streptomyces coelicolor and Mycobacterium tuberculosis, where it binds directly to the principal σ subunit in these organisms. Expand
Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.
The results show that docking accuracy falls off dramatically if one uses an average or apo structure, and it is shown that the drop in docking accuracy mirrors the degree to which the protein moves upon ligand binding. Expand
A general method for exploiting QSAR models in lead optimization.
  • Richard A. Lewis
  • Chemistry, Medicine
  • Journal of medicinal chemistry
  • 11 February 2005
A new protocol for performing automated iterative quantitative structure-activity relationship (QSAR) studies is described and the results of experiments on two QSAR sets from the literature are presented. Expand
Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst
Two main conclusions emerged from the study: first, the faster rule-based methods for conformational analysis give pharmacophore models that are just as good as, and in some cases better than, the models generated using the slower, more rigorous approaches. Expand
Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2)
A genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor to fermentor culture in Modified Evans Media limited cultures finds several genes whose expression patterns are similar to up-regulated members of the GlnR regulon and are induced in response to nitrogen limitation. Expand
Metal templated design of protein interfaces
A rational design approach that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event and provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces. Expand
Control of protein oligomerization symmetry by metal coordination: C2 and C3 symmetrical assemblies through Cu(II) and Ni(II) coordination.
Crystallographic studies indicate that the same four-helix-bundle protein construct, MBPC-1, can self-assemble into C(2) and C(3) symmetrical assemblies dictated by Cu( II) and Ni(II) coordination, respectively, which can be directly applied to biological self-assembly. Expand
Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
This study provides evidence for widespread genetic recombination, rather than it being focussed at 'hotspots', suggesting that the previously proposed 'archipelago model' of genomic differences between S. coelicolor and S. lividans is unduly simplistic. Expand
U-50,488, a selective kappa opioid agonist: Comparison to other reputed kappa agonists
U-50, 488 had no such mu agonist or antagonist effects and thus is a more selective kappa agonist; this compound and its congeners may prove useful in the elucidation of the functions of kappa receptors in the central nervous system. Expand