The present invention relates to a method for preparing a novel antibody library and a library prepared thereby. The antibody library prepared according to the present invention contains antibodies having excellent physical properties against a plurality of antigens, thereby having functional diversity and containing a plurality of unique sequences, and thus can be favorably used as an antibody library.

Methods and compositions related to the selective, specific disruption of multiple ligand-receptor signaling interactions, such as ligand-receptor interactions implicated in disease, are disclosed. These interactions may involve multiple cytokines in a single receptor family or multiple ligand receptor interactions from at least two distinct ligand-receptor families. The compositions may comprise polypeptides having composite sequences that comprise sequence fragments of two or more ligand binding sites. The methods and compositions may involve sequence fragments of two or more ligand binding sites that are arranged to conserve the secondary structure of each of the ligands from which the sequence fragments were taken.

Methods and compositions related to the selective, specific disruption of multiple ligand-receptor signaling interactions, such as ligand-receptor interactions implicated in disease, are disclosed. These interactions may involve multiple cytokines in a single receptor family or multiple ligand receptor interactions from at least two distinct ligand-receptor families. The compositions may comprise polypeptides having composite sequences that comprise sequence fragments of two or more ligand binding sites. The methods and compositions may involve sequence fragments of two or more ligand binding sites that are arranged to conserve the secondary structure of each of the ligands from which the sequence fragments were taken.

Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.

The present disclosure provides a bioretrosynthetic method and system based on an AND-OR tree and single-step reaction template prediction. The method decomposes generation of a retrosynthetic pathway of a target molecule into multiple steps of the single-step reaction template prediction when conducting retrosynthesis on the target molecule. During the single-step reaction template prediction, a substrate molecule of the reaction template predicted in a previous step is used as a product molecule of a current reaction template to be predicted. Molecular characteristics of the product molecule are subjected to custom calculation using a SMILES sequence of the product molecule as an input, to be compatible with various single-step reaction template prediction models. The reaction template is determined according to a prediction result of the model, and extended based on a structure of the AND-OR tree. As a result, a potential synthetic pathway is found for the target molecule.

The present disclosure provides a bioretrosynthetic method and system based on an AND-OR tree and single-step reaction template prediction. The method decomposes generation of a retrosynthetic pathway of a target molecule into multiple steps of the single-step reaction template prediction when conducting retrosynthesis on the target molecule. During the single-step reaction template prediction, a substrate molecule of the reaction template predicted in a previous step is used as a product molecule of a current reaction template to be predicted. Molecular characteristics of the product molecule are subjected to custom calculation using a SMILES sequence of the product molecule as an input, to be compatible with various single-step reaction template prediction models. The reaction template is determined according to a prediction result of the model, and extended based on a structure of the AND-OR tree. As a result, a potential synthetic pathway is found for the target molecule.

The present application is directed to methods and systems for identifying small molecule compounds in mixtures using a library comprising calculated structures and corresponding calculated mass spectral fragmentation patterns of known and/or hypothetical small molecule compounds that may be in the mixture and screening of a mass spectrum of the mixture using the library to identify matching fragmentation patterns. If a mass spectral fragmentation pattern present in the mass spectrum of the mixture matches a calculated fragmentation pattern of one of the known or hypothetical compounds this confirms the identity of a compound in the mixture as the known or hypothetical compound. The method represents a platform method that can be used for a multitude of purposes related to the screening and identification of compounds in mixtures. Therefore the methods and systems of the present application represent an approach that is uniquely capable of navigating chemical space and providing a understanding of desired families and pharmacophores.

The present disclosure relates to a method for predicting the permeability of a stratum corneum lipid matrix to a compound. The method includes providing a model of the stratum corneum lipid matrix including ceramides, free fatty acids, cholesterol and water. The model includes 25-45% total ceramides, based on the molar concentration of all components except water, whereof more than 90% are in extended configuration, and wherein 0-30% of the total ceramides are O-acyl ceramides and 100-70% of the total ceramides are non-O-acyl ceramides. The model also includes 25-45% fatty acid and 25-40% of cholesterol, wherein 1-40% of the cholesterol is located by the fatty acid moeity of the ceramides, and 0.2-6 water molecules per ceramide molecule. The method includes providing molecular designators of the compound and calculating, via means of computer simulations, the predicted permeability using the model and the molecular designators.

The present disclosure relates to a method for predicting the permeability of a stratum corneum lipid matrix to a compound. The method includes providing a model of the stratum corneum lipid matrix including ceramides, free fatty acids, cholesterol and water. The model includes 25-45% total ceramides, based on the molar concentration of all components except water, whereof more than 90% are in extended configuration, and wherein 0-30% of the total ceramides are O-acyl ceramides and 100-70% of the total ceramides are non-O-acyl ceramides. The model also includes 25-45% fatty acid and 25-40% of cholesterol, wherein 1-40% of the cholesterol is located by the fatty acid moeity of the ceramides, and 0.2-6 water molecules per ceramide molecule. The method includes providing molecular designators of the compound and calculating, via means of computer simulations, the predicted permeability using the model and the molecular designators.

The invention relates to methods for modulating the immune function through targeting of CLIP molecules. The result is wide range of new therapeutic regimens for treating, inhibiting the development of, or otherwise dealing with, a multitude of illnesses and conditions, including autoimmune disease, cancer, Alzheimer's disease, allergic disease, transplant and cell graft rejection, HIV infection and other viral, bacterial, and parasitic infection, and AIDS. Methods are also provided for preparing a peptide having the property of being able to displace CLIP by feeding one or more peptide sequences into software that predicts MHC Class II binding regions in an antigen sequence and related products.