Enrichment of ligands for the serotonin receptor using the Shape Signatures approach

Shape Signatures, a new 3-dimensional molecular comparison method, has been adapted to rank ligands of the serotonin receptors. A set of 825 agonists and 400 antagonists together with approximately 10,000 randomly chosen compounds from the NCI database were used in this study. Both 1D and 2D Shape Signature databases were created, and enrichment studies were carried out. Results from these studies reveal that the 1D Shape Signature approach is highly efficient in separating agonists from a mixture of molecules which includes compounds randomly selected from the NCI database taken as inactives. It is also equally effective at separating agonists and antagonists from a pool of active ligands for the serotonin receptor. Parallel enrichment studies using 2D shape signatures showed high selectivity with more restricted coverage due to the high specificity of 2D signatures. The influence of conformational variation of the shape signature on enrichment was explored by docking a subset of ligands into the crystal structure of serotonin N-acetyltransferase. Enrichment studies on the resulting "docked" conformations produced only slightly improved results compared with the CORINA-generated conformations.     

Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring

Docking and scoring are critical issues in virtual drug screening methods. Fast and reliable methods are required for the prediction of binding affinity especially when applied to a large library of compounds. The implementation of receptor flexibility and refinement of scoring functions for this purpose are extremely challenging in terms of computational speed. Here we propose a knowledge-based multiple-conformation docking method that efficiently accommodates receptor flexibility thus permitting reliable virtual screening of large compound libraries. Starting with a small number of active compounds, a preliminary docking operation is conducted on a large ensemble of receptor conformations to select the minimal subset of receptor conformations that provides a strong correlation between the experimental binding affinity (e.g., Ki, IC50) and the docking score. Only this subset is used for subsequent multiple-conformation docking of the entire data set of library (test) compounds. In conjunction with the multiple-conformation docking procedure, a two-step scoring scheme is employed by which the optimal scoring geometries obtained from the multiple-conformation docking are re-scored by a molecular mechanics energy function including desolvation terms. To demonstrate the feasibility of this approach, we applied this integrated approach to the estrogen receptor alpha (ERalpha) system for which published binding affinity data were available for a series of structurally diverse chemicals. The statistical correlation between docking scores and experimental values was significantly improved from those of single-conformation dockings. This approach led to substantial enrichment of the virtual screening conducted on mixtures of active and inactive ERalpha compounds.     

Secondary and Tertiary Structure of Polysaccharides in Solutions and Gels

Many polysaccharide chains can adopt ordered helical and ribbon-like secondary structures. It seems however that these chains are often so stiff and extended that the cooperative interactions necessary for stability in the solvent environment can only be achieved when inter-chain as well as intra-chain interactions are favorable. Hence we commonly find two-or more-stranded associations of helices, of ribbons, or of helices with ribbons. These can be regarded as tertiary and higher levels of structure. The ordered secondary structure characteristically requires a regular repeating sequence of sugar residues, and the termination of this sequence by insertion of a residue of different type may also terminate the secondary structure and hence the association in which it is involved. This is the mechanism by which native polysaccharides may link up to form three dimensional networks, or gels, in which state they perform their natural roles in maintaining the hydration and integrity of biological tissues. For several polysaccharides there is evidence that the mechanism of biological control over the fine topology and properties of the gel network is mediated by enzymes which modify sugar residues at the polymer level to change the pattern of “interrupting” sugar residues.     

The characterization and use of different antibodies against the hsp70 major heat shock protein family for the development of an immunoassay.

The hsp70 family of major stress proteins is composed of several different members exhibiting similar structural and functional properties. In order to obtain an antiserum with wide epitope reactivity, rabbits were immunized with a mixture of native and denatured hsp70 purified from bovine muscle by ATP-affinity chromatography. Screening for antibody specificity was performed by a "sandwich" enzyme linked immunosorbent assay (ELISA). Immunoprecipitation and immunoblotting analyses demonstrated that the polyclonal antiserum obtained by us and a monoclonal antibody raised against a different preparation of antigen recognized the same determinant on the native hsp70 molecule (inducible form). With a different specificity the polyclonal antiserum recognized only the denatured monomers of the other members of the hsp70 family. These results are discussed in relation to the immunological features of the hsp70 molecule and to the development of an immunoassay for the detection of hsp70 in cell and tissue extracts.     

Construction of Graded Covariant GL(m/n) Modules Using Tableaux

Irreducible covariant tensor modules for the Lie supergroups GL(m/n) and the Lie superalgebras gl(m/n) and sl(m/n) are obtained through the use of Young tableaux techniques. The starting point is the graded permutation action, first introduced by Dondi and Jarvis, on V ^l . The isomorphism between this group of actions and the symmetric group S _l enables the graded generalization of the Young symmetrizers, and hence of the column relations and Garnir relations, to be made. Consequently, corresponding to each partition of l an irreducible GL(m/n) module may be obtained as a submodule of V ^l . A basis for the module labeled by the partition is provided by GL(m/n)–standard tableaux of shape defined by Berele and Regev. The reduction of an arbitrary tableau to standard form is accomplished through the use of graded column relations and graded Garnir relations. The standardization procedure is algorithmic and allows matrix representations of the Lie superalgebras gl(m/n) and sl(m/n) to be constructed explicitly over the field of rational numbers. All the various steps of the standardization algorithm are exemplified, as well as the explicit construction of matrices representing particular elements of gl(m/n) and sl(m/n).     

Polynomial neural network for linear and non-linear model selection in quantitative-structure activity relationship studies on the internet

This article presents a self-organising multilayered iterative algorithm that provides linear and non-linear polynomial regression models thus allowing the user to control the number and the power of the terms in the models. The accuracy of the algorithm is compared to the partial least squares (PLS) algorithm using fourteen data sets in quantitative-structure activity relationship studies. The calculated data show that the proposed method is able to select simple models characterized by a high prediction ability and thus provides a considerable interest in quantitative-structure activity relationship studies. The software is developed using client-server protocol (Java and C++ languages) and is available for world-wide users on the Web site of the authors.     

Multipoint boundary value problems with discontinuities II. Convergence of the initial value adjusting method

In this paper we give a proof for convergence of the initial value adjusting method, described in detail in part I, based on Kantorovich's theorem. Under standard assumptions on the dynamics, boundary conditions, and initial approximations, a quadratic convergence rate is obtained.     

Integral equation formulation for buoyancy-driven convection problems

An integral equation formulation for buoyancy-driven convection problems is developed and illustrated. Buoyancy-driven convection in a bounded cylindrical geometry with a free surface is studied for a range of aspect ratios and Nusselt numbers. The critical Rayleigh number, the nature of the cellular motion, and the heat transfer enhancement are computed using linear theory. Green's functions are used to convert the linear problem into linear Fredholm integral equations. Theorems are proved which establish the properties of the eigenvalues and eigenfunctions of the linear integral operator which appears in these equations.     

Low-level flow-induced acoustic resonances in ducts

Acoustic resonances are generated by air moving past a plate with a semi-circular leading edge located in a duct. The sound stimulates the small separation bubble near the leading edge to shed vortices into the boundary layer at the sound frequency. The acoustic energy required to sustain the resonances is generated as these vortices pass the trailing edge of the plate.