A method and system for calculating the free energy difference between a target state and a reference state. The method includes determining one or more intermediate states using a coupling parameter, performing molecular simulations to obtain ensembles of micro-states for each of the system states, and calculating the free energy difference by an analysis of the ensembles of micro-states of the system states. The method can be particularly suited for calculating physical or non-physical transformation of molecular systems such as ring-opening, ring-closing, and other transformations involving bond breaking and/or formation. A soft bond potential dependent on a bond stretching component of the coupling parameter and different from the conventional harmonic potential is used in the molecular simulations of the system states for the bond being broken or formed during the transformation.

A method and system for calculating the free energy difference between a target state and a reference state. The method includes determining one or more intermediate states using a coupling parameter, performing molecular simulations to obtain ensembles of micro-states for each of the system states, and calculating the free energy difference by an analysis of the ensembles of micro-states of the system states. The method can be particularly suited for calculating physical or non-physical transformation of molecular systems such as ring-opening, ring-closing, and other transformations involving bond breaking and/or formation. A soft bond potential dependent on a bond stretching component of the coupling parameter and different from the conventional harmonic potential is used in the molecular simulations of the system states for the bond being broken or formed during the transformation.

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

This invention relates to the identification of peptide binding to ligands, and in particular to identification of epitopes expressed by microorganisms and by mammalian cells. The present invention provides polypeptides comprising the epitopes, and vaccines, antibodies and diagnostic products that utilize or are developed using the epitopes.

The disclosure provides a process of designing and optimizing supramolecular therapeutics. The disclosure also provides a method for designing and optimizing antibody drug conjugates.

The disclosure provides a process of designing and optimizing supramolecular therapeutics. The disclosure also provides a method for designing and optimizing antibody drug conjugates.

The method for protein selection can include: characterizing a protein set, training a prediction model, determining target characteristic values, and determining a candidate protein set based on the target characteristic values.

A device for creating a fragment model from a crystal model is equipped with a division position identifying section adapted for identifying multiple division atom pairs for multiple atoms contained in the crystal model. The atoms in the division atom pairs are contained in different fragment models. The device is additionally equipped with a model creating section adapted for identifying each of multiple atom groups each composed of atoms bonded to each other in the crystal model and for creating fragment models respectively corresponding to the identified atom groups.

A device for creating a fragment model from a crystal model is equipped with a division position identifying section adapted for identifying multiple division atom pairs for multiple atoms contained in the crystal model. The atoms in the division atom pairs are contained in different fragment models. The device is additionally equipped with a model creating section adapted for identifying each of multiple atom groups each composed of atoms bonded to each other in the crystal model and for creating fragment models respectively corresponding to the identified atom groups.

Provided are a method for searching for a molecular stable structure, a program for searching for a molecular stable structure, and a device for searching for a molecular stable structure, which are capable of acquiring a stable structure and various locally stable structures from a structural formula of a compound in a short time and with high accuracy. A three-dimensional structure is generated from the structural formula of the compound, and a locally stable structure is obtained from the three-dimensional structure. A one-dimensional or multidimensional energy distribution function for one or a plurality of internal coordinates and a probability distribution function of increasing a probability of low-energy internal coordinates are calculated from internal coordinates and an energy value of the locally stable structure. The method for searching for a molecular stable structure repeats the following processes: generating a three-dimensional structure based on the calculated probability distribution function; acquiring a locally stable structure; reflecting internal coordinates and an energy value of the obtained locally stable structure on the energy distribution function and the probability distribution function; and acquiring the locally stable structure, thereby obtaining a plurality of the locally stable structures and a structure with lowest energy. The program and the device for searching for a molecular stable structure execute the method.