Abstract: Techniques for analyzing one or more protein structures. In one aspect of the invention, the technique comprises the following steps. A normalized second-order hydrophobic moment is determined for a protein structure. The normalized second-order hydrophobic moment is then used for analysis of the protein structure. A scoring function in accordance with the normalized second-order hydrophobic moment for the protein structure may be determined. A score for the protein structure may then be generated using the scoring function. The scoring function may represent an integral of the normalized second-order hydrophobic moment. The scores may be generated for a plurality of protein structures. The scores generated for the plurality of protein structures may then be compared.

Abstract: Cosmetic or pharmaceutical preparations which are distinguished by an effective content of one or more monomeric or homo- or heterodimer or homo- or heterotrimeric or homo- or heterotetrameric oligopeptides, where these oligopeptides are based on a structure Val-Val-Arg-Pro SEQ ID NO:1 as homo- or heteromonomer.

Abstract: Described herein are methods for registering analytical images comprising obtaining an image of an array, wherein the image depicts fiducials that can be used to register the sequential images of the array by determining the average intensity of the fiducials and then positioning the sequential images such that the average intensity of the fiducials attains either a maximum or minimum value.

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: A process is provided for isolating a protein component of animal muscle tissue by mixing a particulate form of the tissue with an acidic aqueous liquid having a pH below about 3.5 to produce a protein rich solution substantially free of myofibrils and sarcomere tissue structure. The protein rich aqueous solution can be treated to effect protein precipitation, followed by protein recovery.

Abstract: Protein geranylgeranyl transferase type I (GGTase-I), a Ca1a2X prenyltransferase, is an essential enzyme in eukaryotes. GGTase-I catalyzes the carboxyl-terminal lipidation of over one hundred proteins, including many GTP-binding regulatory proteins (G proteins). The presently disclosed subject matter comprises a plurality of crystal structures of mammalian GGTase-I in complex with substrates and products that provide the first structural information for this enzyme, facilitating the elucidation of a generalized method of action for all protein prenyltransferases; the method includes a role in product transport. The structures reveal specificity determinants that allow classification of putative protein prenyltransferase sequences and can facilitate optimization of GGTase-I and FTase modulators.

Abstract: A polymer is prepared by self-assembly of a plurality of monomeric polypeptide units. The polymer tends to form a nanotube and is capable of encapsulating a particular drug molecule. Once encapsulated in the polymer of the present invention, the drug molecule may be delivered to a particular location of human body to effectively cure a disease or treat a symptom. Generally, the monomeric polypeptide unit of the present invention has a sequence found in Pyrodictium abyssi, a microorganism that produces an extracellular network having hollow protein tubes, or a sequence substantially identical thereto. The monomeric polypeptide may be mass produced using recombinant biotechnologies and be polymerized into the polymer of the present invention. One or more additional targeting vector may be attached to the monomeric polypeptide unit or the polymer to facilitate the targeting of the drug molecule that may be held there within.

Abstract: The present invention relates to the three dimensional solution structure of the N-terminal domain of TNFR-1 associated death domain protein (“N-TRADD”), as well as the identification and characterization of a C-TRAF2 binding active site of N-TRADD. Also provided for by the present invention are methods of utilizing the three dimensional structures for the design and selection of potent and selective inhibitors of TNF signaling pathways.

Abstract: The present invention relates to methods of inhibiting angiogenesis associated with a disease or disorder with peptides homologous to amino acid residues 130-137 or 132-139 of human troponin subunit I.

Abstract: Provided are means for evaluating and identifying putative substrates of the twin arginine translocation (Tat) secretory pathway in Streptomyces and other bacterial species. Also provided, therefore, are simple ways to express, secrete and purify correctly folded heterologous proteins on a large scale using host microorganisms, such as, Streptomyces and the Tat pathway therein. Many of the thus-produced proteins are of significant therapeutic value in the pharmaceutical and biochemical industries, particularly when they can be secreted from the host in fully-folded active form. Accordingly, there are further provided the heterologous proteins produced by the Tat secretion pathway using the foregoing methods, and the computer algorithm used to identify the Tat signal sequence and putative substrates.

Abstract: This invention relates to a novel approach for identification of T-cell epitopes, that give rise to an immune reaction in a living host. By means of this novel method biological compounds can be generated which have a no or at least a reduced immunogenicity when exposed to the immune system of a given species and compared with the relevant non-modified entity. Thus the invention relates also to novel biological molecules, especially proteins and antibodies, obtained by the method according to the invention.

Abstract: The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted CD84-like polypeptide. These polynucleotides comprise nucleic acid sequences isolated from cDNA library from human spleen (Hyseq clone identification numbers 2938352 (SEQ ID NO: 1)). Other aspects of the invention include vectors containing processes for producing novel human secreted CD84-like polypeptides, and antibodies specific for such polyeptides.

Abstract: A computational method for identifying adhesin and adhesin-like proteins, said method comprising steps of computing the sequence-based attributes of a neural network software wherein the attributes are (i) amino acid frequencies, (ii) multiplet frequency, (iii) dipeptide frequencies, (iv),charge composition, and (v) hydrophobic composition, training the artificial neural Network (ANN) for each of the computed five attributes, and identifying the adhesin and adhesin-like proteins having probability of being an adhesin (Pad) as ?0.51; a computer system for performing the method; and genes and proteins encoding adhesin and adhesin-like proteins.

Abstract: A computer-implemented method for determining an optimal treatment protocol for a disease related to angiogenesis, comprising creating an angiogenesis model including pro-angiogenic and anti-angiogenic factors. Effective vessel density (EVD) is incorporated as a factor regulating switching on and switching off of at least one component in the angiogenesis model. Effects of vasculature maturation and mature vessel destabilization are incorporated. Pro-angiogenic and anti-angiogenic factors, which can influence changes in state of a tissue, are selected. Effects of drugs in the pro-angiogenic and anti-angiogenic factors are incorporated. A plurality of treatment protocols in a protocol space is generated. A best treatment protocol based on a pre-determined criteria is selected.

Abstract: The present invention is a multiparameter method of screening for the diagnosis, prevention or treatment of atherosclerosis-related coronary heart disease (CHD) or stroke. This method is used for predicting a total risk of the disease and a disease risk level, determining a primary cause in the disease, assessing a therapeutic efficacy and optimizing the therapeutic targets at the different stages of the disease in different individuals who require the therapy to prevent or to treat the disease. The method of this invention can be used to combine the contributions of atherosclerotic risk factors to the disease and to unite the two major methods for diagnosing the disease: screening the Low-density lipoprotein (LDL) level and measuring the C-reactive protein (CRP) concentration in human blood. The method of this invention is written as an executable computer program named the MMA.exe © 2004, by Xing F. Wang, which provides greater ease and convenience to perform this method.

Abstract: A method implemented in the form of a computer simulation code for evaluating the free energy of binding between polypeptide amino acid residues and one or more molecular fragment types is presented. The basis of the method is a novel weighted Metropolis Monte Carlo approach for sampling the grand canonical ensemble. By making use of the properties of the grand canonical ensemble, the affinity of fragments for binding in the vicinity of each protein residue can be efficiently computed. The binding volume associated to each fragment-residue pair is estimated on the basis of a simple proximity criteria, and a useful affinity mapping of the protein surface can be obtained in this way. The analysis of such data for various fragment types provides valuable information to help identify protein binding sites, as well as to identify key fragments used for building potential drug leads.

Abstract: The present invention relates to systems, methods, and computer program products for the analysis of gene expression data, especially data that have been acquired using microarray technologies. In particular, the present invention relates to methods for analyzing a set of genes that have been partitioned into disjoint subsets known as clusters. It describes methods for quantitatively evaluating the quality of gene clustering, based on the extent to which the similarity of documents associated with genes in a cluster collectively distinguish that cluster from all the other clusters, as well as the extent to which words and phrases, present in documents associated with genes in the cluster, collectively distinguish that cluster from all the other clusters.

Abstract: The present invention relates to polypeptides which comprise the ligand binding domain of Lck, crystalline forms of these polypeptides, and the use of these crystalline forms to determine the three dimensional structure of the catalytic domain of Lck. The invention also relates to the use of the three dimensional structure of the Lck catalytic domain both alone, or in complex with inhibitors, in methods of designing and/or identifying potential inhibitors of Lck activity, for example, compounds which inhibit the binding of a native substrate to the Lck catalytic domain. The invention also relates to the use of the three dimensional structure of the Lck catalytic domain both alone, or in complex with inhibitors, in methods of designing and/or identifying potential selective inhibitors of Lck activity, for example, compounds which inhibit the binding of a native substrate to the Lck catalytic domain selectively.

Abstract: The present invention relates to pharmaceutical compositions comprising therapeutically effective amounts of fragments or homologs of troponin C, I or T subunits for the treatment of diseases or disorders involving abnormal angiogenesis.

Abstract: Methods for the diagnosis and evaluation of stroke and stroke sub-type employ a variety of bio-markers including cellular fibronectin (c-Fn) assembled as a panel for stoke diagnosis and evaluation. Methods are disclosed for selecting markers and correlating their combined levels with a clinical outcome of interest. In various aspects the methods permit early detection and differentiation of stroke subtypes, determination of the prognosis of a patient presenting stroke symptoms, and identification of a patient at risk for early hematoma growth and/or malignant massive cerebral artery infarction. The disclosed methods provide rapid, sensitive and specific assays to greatly increase the number of patients that can receive beneficial stroke treatment and therapy, and to reduce the human and economic costs associated with incorrect stroke diagnosis.