Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from the sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from the sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: Present invention concerns amplification protocols and hairpin-harbouring primer pairs suitable for multiplex applications, preferably in closed automated systems. In particular, presented herein protocols allow one-tube multiplex amplification of a potentially large amount of targets in a manner that allows to readily tag the products of said amplification with indexes, unique molecular identifiers (UMIs), or other NGS-related tags compatible with different NGS strategies and platforms.

Abstract: The present invention relates to a highly automatable method for isolation and/or purification of nucleic acids from a biological sample, which is particularly suitable for nucleic acids-shorter than 250 bp and can be performed without a proteolytic pre-digestion step in an automated system, preferably a cartridge-based system. In a further aspect, the present invention also provides automated nucleic acid detection methods based on said isolation and/or purification method, as well as buffers and kits to be used in performing said methods.

Abstract: The present invention relates to a highly automatable method for isolation and/or purification of nucleic acids from a biological sample, which is particularly suitable for nucleic acids-shorter than 250 bp and can be performed without a proteolytic pre-digestion step in an automated system, preferably a cartridge-based system. In a further aspect, the present invention also provides automated nucleic acid detection methods based on said isolation and/or purification method, as well as buffers and kits to be used in performing said methods.

Abstract: The present invention generally-relates to cartridges for automated systems and automated methods for fully automated processing of biological samples to next-generation sequencing-ready nucleic acid libraries. In particular, the present invention concerns a fluidic cartridge comprising a compartment for receiving a biological sample, means for liberating and/or purifying nucleic acids from the received sample and for transporting said nucleic acids to a compartment wherein NGS library can be prepared from said nucleic acids using provided therein reagents. In a particular aspect, the present invention also concerns cartridges for automated systems and automated methods for preparing an NGS nucleic acid library from a biological sample simultaneously or sequentially with a qPCR assay performed on the same biological sample.

Abstract: The present invention generally concerns an automated system capable of performing quantitative PCR (qPCR) analysis of a nucleic acid present in a biological sample together with preparation of a sequencing-ready nucleic acid library from said sample, either simultaneously or sequentially. In a further aspect, the present invention also provides a method for performing qPCR of a nucleic acid present in a biological sample together with simultaneous of sequential preparation of a sequencing-ready nucleic acid library from said sample. Finally, the present invention also provides removable cartridges for use in the automated systems and methods according to the invention.

Abstract: The invention provides methods for the production of single-chain Alphabody polypeptides having detectable binding affinity for, or detectable in vitro activity on, a viral protein of interest, which comprising the step of producing a single-chain Alphabody library comprising at least 100 different-sequence single-chain Alphabody polypeptides, wherein said Alphabody polypeptides differ from each other in at least one of a defined set of 5 to 20 variegated amino acid residue positions, and wherein said variegated amino acid residue positions are located at specific positions in one or more of the alpha-helices of the Alphabody or the linker fragment connecting two consecutive alpha-helices of the Alphabody polypeptides. The invention further provides Alphabodies obtainable by the methods of the invention and uses thereof.

Abstract: Alphabodies that specifically bind to cytokines or growth factor and/or their receptors, as well as polypeptides that comprise or essentially consist of such Alphabodies. Further nucleic acids encoding such Alphabodies; methods for preparing such Alphabodies and polypeptides; host cells expressing or capable of expressing such Alphabodies and polypeptides; compositions, and in particular pharmaceutical compositions, that comprise such Alphabodies, polypeptides, nucleic acids and/or host cells; and uses of such Alphabodies or polypeptides, nucleic acids, host cells and/or compositions, in particular for prophylactic, therapeutic or diagnostic purposes.

Abstract: Single-chain Alphabodies that comprise an alpha-helical binding region which mediates binding to a first fusion-driving region of a class-1 viral fusion protein and which structurally mimics a second fusion-driving region of said class-1 viral fusion protein, wherein said first and second fusion-driving regions of said class-1 viral fusion protein are regions which interact to drive the fusion between a virus displaying said class-1 viral fusion protein and a target cell.

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 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 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.