Abstract: The present invention relates to the determination of intra- or intermolecular interaction between molecules in aqueous solution, the method comprising the steps of: (a) determining the dehydration of all atoms in the intermolecular interface, (b) adding the vacuum hydrogen bond energy, and (c) further adding the change in the free enthalpy of the interacting partners upon their interaction. The obtained results can be used for the prediction if and to what extent two molecules of various origin fit to each other.

Abstract: Techniques for determining an equilibrium structure of a protein in a predetermined environment, the protein having Ramachandran angles and a known denatured structure, are disclosed. One example method includes determining a maximum RMS volume of the known denatured structure of the protein and calculating at least one force on the protein in its current structure in the predetermined environment. The net torque resulting from the at least one force for each of the Ramachandran angles of the protein is then determined. Then at least one section of the protein structure on a side of a Ramachandran angle with the greatest torque is rotated to form a new structure. A RMS volume for the new structure is then calculated, and the method is repeated using the new structure until the new RMS volume of the new protein structure is not less than the RMS volume of the starting structure.

Abstract: The present invention relates generally to structural studies of the insulin binding site of the insulin receptor (IR) and the insulin-like growth factor 1 receptor (IGF-1R). More particularly, the present invention relates to the crystal structure of the low affinity insulin binding site of the IR ectodomain comprising the C-terminal region of the IR ?-chain, as well as the corresponding region of IGF-1R, and to methods of using the crystal and related structural information to screen for and design compounds that interact with or modulate the function of IR and/or IGF-1R.

Abstract: A novel metric, termed cluster resolution, which compares the separation of clusters of data points while simultaneously considering the shapes of the clusters and their relative orientations. This metric, in conjunction with an objective variable ranking metric, allows for the fully-automated determination of the optimal number of variables to be included in a chemometric model of a system. Cluster resolution is based upon considering the minimum distance between (or the extent of overlap of) confidence ellipses constructed around clusters of points representing different classes of objects. This approach can be generally applied to feature selection for a variety of applications and represents a significant step towards the development of fully-automated, objective construction of chemometric models.

Abstract: A method of estimating the cross-sectional area of a molecule for use in the prediction of ion mobility gives gas phase interaction radii determination and cross-sectional algorithm computation to provide separation and characterization of structurally related isomers. More specifically, the invention provides a method of correlating the differences in the molecular structures with differences in anti-cancer activity of pre-determined anti-cancer drugs by utilizing a new algorithm for estimating the cross-sectional area of the molecules of such drugs.

Abstract: The present invention relates to isolated Porphyromonas gingivalis polypeptides and nucleotides. The polypeptides include an amino acid sequence selected from the group consisting of: SEQ. ID. NO. 110; SEQ. ID. NO. 111; SEQ. ID. NO. 112; SEQ. ID. NO. 113; SEQ ID NO: 120; SEQ. ID. NO. 123; SEQ. ID. NO. 124; SEQ. ID. NO. 125; SEQ. ID. NO. 130; SEQ. ID. NO. 131; SEQ. ID. NO. 132; SEQ. ID. NO. 133; SEQ. ID. NO. 135; SEQ. ID. NO. 136; SEQ. ID. NO. 137; SEQ. ID. NO. 138; SEQ. ID. NO. 143; SEQ. ID. NO. 144; SEQ. ID. NO. 145; SEQ. ID. NO. 146; SEQ. ID. NO. 147; SEQ. ID. NO. 148; and amino acid sequences at least 95% identical thereto.

Abstract: Ambulatory or in-hospital monitoring of patients is provided with early warning and prioritization, enabling proactive intervention and amelioration of both costs and risks of health care. Multivariate physiological parameters are estimated by empirical model to remove normal variation. Residuals are tested using a multivariate probability density function to provide a multivariate health index for prioritizing medical effort.

Abstract: The invention relates to the field of compounds, especially peptides or polypeptides, that have thrombopoietic activity. The peptides and polypeptides of the invention may be used to increase platelets or platelet precursors (e.g., megakaryocytes) in a mammal.

Abstract: Isolated peptides that are fragments of protein products arising from frameshift mutations in genes associated with cancer are disclosed. The isolated peptides of the invention are capable of eliciting T cell immunity against cells harboring genes with such frameshift mutations. Cancer vaccines and therapeutically effective compositions containing the peptides of the inventions are also described.

Abstract: A method for performing a molecular dynamics simulation for determining the solvent accessible surface area of a molecule with respect to atomic coordinates, the molecule comprising a plurality of atoms, a sphere being assigned to each atom, and each sphere comprising a radius and a center position.

Abstract: The present invention relates to processes for the screening, preparation and characterization of (R)-selective ?-transaminases, to transaminases obtained thereby and their uses in various transamination processes.

Abstract: The invention provides novel mutations, mutation combinations or mutational profiles of HIV-1 reverse transcriptase and/or protease genes correlated with phenotypic resistance to HIV drugs. More particularly, the present invention relates to the use of genotypic characterization of a target population of HIV and the subsequent correlation of this information to phenotypic interpretation in order to correlate virus mutational profiles with drug resistance. The invention also relates to methods of utilizing the mutational profiles of the invention in databases, drug development, i.e., drug design, and drug modification, therapy and treatment design, clinical management and diagnostic analysis.

Abstract: Structural and functional analysis of peptide inhibitor binding to the cyclin D1 groove has been investigated and used to design peptides that provide the basis for structure-activity relationships, have improved binding and have potential for development as chemical biology probes, as potential diagnostics and as therapeutics in the treatment of proliferative diseases including cancer and inflammation.

Abstract: The system and method for predicting and measuring a subject's analgesic state and analgesic adequacy. Biopotential signals are obtained from a subject through electrodes. A processor will compute a measure that is representative of the subject's sedative state and/or muscle activity. A metric representative of such measures is then determined. In the case where a measure is taken of both the subject's sedative state and muscle activity the two measures are combined into an index representative of the subject's analgesic state and analgesic adequacy.

Abstract: The present invention is related to a quantitative structure-based affinity scoring method for peptide/protein complexes. More specifically, the present invention comprises a method that operates on the basis of a highly specific force field function (e.g. CHARMM) that is applied to all-atom structural representations of peptide/receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. The method of the invention further comprises a de novo approach to estimate dehydration energies from the simulation of individual amino acids in a solvent box filled with explicit water molecules and applying the same force field function as used to evaluate peptide/receptor complex interactions.

Abstract: An ionic complex precipitate comprising a hedgehog protein and deoxycholate whereby the forming of the complex does not enhance the solubility of said protein, is suitable for increasing the activity of the protein and/or for the delayed release of the protein.

Abstract: A method of scoring binding affinity of a proposed ligand molecule for a receptor molecule using a computer and computer data bases, which accounts for the increase in energy required where docking disrupts water molecules that are localized at ligand hydration sites. The method uses computer-stored data representing a predicted ligand-receptor structure (preferably one that is validated). The computerized scoring analysis includes determining whether the receptor includes one or more hydration sites occupied by localized water, and, if so, assessing a penalty if docking the ligand into the receptor results in unfavorable interaction of the ligand with a localized water molecule remaining at the receptor hydration site (i.e. after docking).

Abstract: A probabilistic digital signal processor using data from multiple instruments is described. Initial probability distribution functions are input to a dynamic state-space model, which operates on state and/or model probability distribution functions to generate a prior probability distribution function, which is input to a probabilistic updater. The probabilistic updater integrates sensor data from multiple instruments with the prior to generate a posterior probability distribution function passed (1) to a probabilistic sampler, which estimates one or more parameters using the posterior, which is output or re-sampled in an iterative algorithm or (2) iteratively to the dynamic state-space model. For example, the probabilistic processor operates on fused data using a physical model, where the data originates from a mechanical system or a medical meter or instrument, such as an electrocardiogram or pulse oximeter to generate new parameter information and/or enhanced parameter information.

Abstract: Disclosed in this specification is a method for identifying at least one aptamer that can bind to a bio-molecular target. The aptamer is designed in silico based on the structure of the target molecule. The process includes the steps of determining a first seed residue and growing an oligomer, one residue at a time, while maximizing the entropy of target-oligomer complex or minimizing the binding energy after the addition of each oligomer.

Abstract: Disclosed herein are methods of estimating an analyte concentration which include generating a signal indicative of the analyte concentration, generating a signal indicative of a temperature, generating a signal indicative of a pH, and transforming the signal indicative of the analyte concentration utilizing an equation of the form of a modified Michaelis-Menten equation depending on Michaelis-Menten parameters, wherein values of the Michaelis-Menten parameters are set based upon data which includes temperature and pH calibration parameters, the signal indicative of a temperature, and the signal indicative of a pH. Also disclosed herein are measurement devices which employ the aforementioned methods.