Crystal structure and Hirshfeld surface analysis of 3-(bromo-meth-yl)-2-[1,2-di-bromo-2-(6-nitro-benzo[][1,3]dioxol-5-yl)eth-yl]-1-(phenyl-sulfon-yl)-1-indole chloro-form 0.585-solvate.

The title indole derivative, CHBrNOS, crystallizes with a partial occupancy [0.585 (4)] CHCl solvent mol-ecule. The dihedral angles between the indole ring system and pendant nitro-benzodioxolane rings system and phenyl-sulfonyl ring are 4.

Sanggenol B, a plant bioactive, as a safer alternative to tackle cancer by antagonising human FGFR.

Fibroblast Growth Receptor Factor (FGFR) are a family of proteins which are, in addition to their biological role, are involved in various pathological functions, such as cancer cellular proliferation, and metastasis. Deregulation of FGFRs at various points could result in malignancy. A conformational transition of the DFG (Asp-Phe-Gly) motif can switch the enzyme from a catalytically active (DFG-in) to an inactive (DFG-out) state.

Crystal structure of d(CCGGGGTACCCCGG) at 1.4 Å resolution.

The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG) is reported at 1.4 Å resolution in the tetragonal space group P422. The sequence was designed to fold as a four-way junction.

DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC).

High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals.

The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences.

The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues.

Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor.

Proteins embody epitopes that serve as their antigenic determinants. Epitopes occupy a central place in integrative biology, not to mention as targets for novel vaccine, pharmaceutical, and systems diagnostics development. The presence of T-cell and B-cell epitopes has been extensively studied due to their potential in synthetic vaccine design.

Structure of d(CCCCGGTACCGGGG)2 at 1.65 Å resolution.

The crystal structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 has previously been reported as an A-type double helix at a resolution of 2.5 Å in space group P41. Here, the structure of this sequence was determined at a significantly higher resolution of 1.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of carbonyl reductase from Candida parapsilosis ATCC 7330.

The NAD(P)H-dependent carbonyl reductase from Candida parapsilosis ATCC 7330 catalyses the asymmetric reduction of ethyl 4-phenyl-2-oxobutanoate to ethyl (R)-4-phenyl-2-hydroxybutanoate, a precursor of angiotensin-converting enzyme inhibitors such as Cilazapril and Benazepril. The carbonyl reductase was expressed in Escherichia coli and purified by GST-affinity and size-exclusion chromatography. Crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to 1.

Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: new insights into solvent interactions.

The crystal structure of the decamer sequence d(CCGGGACCGG)(4) has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.

Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex.

The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction.

Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK).

Understanding the principles of protein receptor recognition, interaction, and association with molecular substrates and inhibitors is of principal importance in the drug discovery process. MOLSDOCK is a molecular docking method that we have recently developed. It uses mutually orthogonal Latin square sampling (together with a variant of the mean field technique) to identify the optimal docking conformation and pose of a small molecule ligand in the appropriate receptor site.

MOLS sampling and its applications in structural biophysics.

This review describes the MOLS method and its applications. This computational method has been developed in our laboratory primarily to explore the conformational space of small peptides and identify features of interest, particularly the minima, i.e.

An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins.

Background: The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.

Methodology: We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface.

T-h-2 immunity and CD3+CD45RBlow-activated T cells in mice immunized with recombinant bacillus Calmette-Guérin expressing HIV-1 principal neutralizing determinant epitope.

The genetic engineering of Mycobacterium bovis-bacillus Calmette-Guérin to express foreign epitopes is an attractive strategy in the field of epitope vaccines. We constructed an 'epitope-trap vector' with Mycobacterium tuberculosis chaperonin-10 as a carrier antigen and used it to express the HIV-1 principal neutralizing determinant epitope. We also identified a new chaperonin-10 promoter that was hyperexpressive compared with the heat shock protein-65 promoter.

MOLS--a program to explore the potential energy surface of a peptide and locate its low energy conformations.

We describe a computer program that uses mutually orthogonal Latin squares (MOLS) to perform an efficient and exhaustive conformational search of the multi-dimensional potential energy hypersurface of an oligopeptide, and locate all its low energy conformations. The software package has been developed with a user-friendly graphical interface using the Fast Light Tool Kit (FLTK)--a cross platform C++ toolkit.

Amino acid variation in cellular processes in 108 bacterial proteomes.

We have analysed 108 bacterial proteomes in the KEGG database to explore the variation of amino acid composition with respect to protein function. The ratio between the observed amino acid composition and that predicted based on mononucleotide composition was calculated for each functional category. This indicated whether the compositional variation arose from mutation or selection pressure.