Abstract: The present invention provides methods and apparatus for analyzing a protein structure.

Abstract: The present invention provides methods and apparatus for analyzing a protein structure.

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: The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immuno-therapeutic agents.

Abstract: The invention provides methods and apparatus for analyzing a protein structure by A) receiving a reference structure (A) forming a three dimensional representation of a protein; B) substituting into the structure of (A) a pattern with amino-acids different from the one of the protein; C) optimizing the conformation of (A) substituted by pattern of (B); D) assessing the energetic compatibility (EC) of the pattern of (B) within the context of the structure of (A) being structurally optimized in (C) with respect to the pattern, by comparing the global energy of the substituted and optimized protein structure with the global energy of the non-substituted reference structure; and E) storing a value reflecting the EC of the pattern together with information related to the structure of the pattern in the form of an energetic compatibility object (ECO).

Abstract: The invention relates to a method for producing a mixture comprising two or more different antibodies in a single recombinant host cell. In one embodiment, a mixture of different monovalent antibodies is produced. In another embodiment, a mixture of monovalent and bivalent antibodies is produced. The invention also relates to mixtures of antibodies obtainable by the method of the invention and to light chain sequences that are particularly useful in the method of the invention.

Abstract: The present invention provides methods and apparatus for analyzing a protein structure.

Abstract: A method for generating information related to the molecular structure of a biomolecule, comprising the steps of: (a) receiving a three-dimensional representation of said molecular structure, comprising a first set of residue portions and a template; and (b) modifying the representation of step (a) by at least one optimization cycle.

Abstract: The present invention is related to a non-natural, thermodynamically stable, proteinaceous scaffold consisting of three non-covalently associated peptides, wherein each peptide sequence comprises less than fifty amino acid residues and wherein at least 50% of the said residues are substitutable amino acids into at least ten different amino acid residue types. The present invention is further related to a non-natural, triple-stranded, parallel alpha-helical coiled coil scaffold wherein each of the three constituting peptide sequences comprise between 2 and 7 consecutive heptad repeats, wherein at least 50% of the core residues are isoleucines, wherein all non-core residues are alanines, and wherein the constituting peptide sequences remain associated under physical conditions that are significantly different from physiological conditions.

Abstract: The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.

Abstract: The present invention is directed to peptides, and nucleic acids encoding them, derived from the Hepatitis C Virus (HCV). The peptides are those which elicit a CTL and/or HTL response in a host. The invention is also directed to compositions and vaccines for prevention and treatment of HCV infection and diagnostic methods for detection of HCV exposure in patients.

Abstract: The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.

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: The present invention relates to a method for structure-based prediction of properties of peptides and peptide analogs in complex with major histocompatibility (MHC) class I and class II molecules. The said properties mainly relate to the three-dimensional structure of an MHC/peptide complex and the binding affinity of a peptide for an MHC receptor. The invention further relates to a computer program and a device therefor. The invention further relates to data produced by a method of the invention. The invention further relates to peptides and peptide analogs predicted to bind to target-MHC molecules. The present invention thus relates to the field of immunology, with possible applications in manufacture of vaccinates, de-immunization of proteins, and manufacture of therapeutic agents, especially immunotherapeutic agents.

Abstract: The present invention is directed to peptides, and nucleic acids encoding them, derived from the Hepatitis C Virus (HCV). The peptides are those which elicit a CTL and/or HTL response in a host. The invention is also directed to compositions and vaccines for prevention and treatment of HCV infection and diagnostic methods for detection of HCV exposure in patients.

Abstract: The present invention is related to an isolated polypeptide micro-scaffold displaying immunoglobulin CDR2 or CDR3 polypeptide sequences, comprising a CDR2 or CDR3 polypeptide sequence interconnecting fragments of the adjacent framework polypeptide sequences, which are arranged to form two anti-parallel ?-strands. The present invention is further related to a method to search, select or screen for immunoglobulin CDR2 or CDR3 polypeptide sequences that bind to a given antigen or mixture of antigens, comprising the steps of: Creating a CDR library with the method of claim 13 from the genetic information of an individual or group of individuals; Select a CDR, which binds to said antigen or mixture of antigens.

Abstract: An in vitro method for constructing a concatenated head-to-tail repertoire of target nucleic acid sequences is revealed. In particular, the method relates to cycles of concatenation whereby after a single cycle of concatenation, not more than two identical copies of each target nucleic acid sequence are linked together head-to-tail on the same molecule of DNA. The present method ensures that each molecule of a concatenated repertoire is derived from a single template target sequence of the starting repertoire.

Abstract: Compounds derived from BPTI which inhibit factor VIIa-TF complex with an inhibition constant of less than 500 nM, their pharmaceutical compositions, and methods of use. Also disclosed are isolated nucleic acid segments encoding for the compounds, vectors comprising the nucleic acid segment and promoter, transformed host cells, and a method for preparing the compounds using transformed host cells.

Abstract: A compound derived from BPTI which inhibits Factor Xa with an inhibition constant less than 50 nM.

Abstract: A method for selecting amino acid residues is disclosed which upon replacement will give rise to an enzyme with an altered pH optimum. The method is specific for metalloenzymes which are inactivated at low pH due to the dissociation of the metal ions. The method is based on altering the pK.sub.a of the metal coordinating ligands or altering the K.sub.ass for the metal binding. New glucose isomerases with an altered pH optimum are provided according to this method. These altered properties enable starch degradation to be performed at lower pH values.