In an embodiment, the present disclosure provides a method of computationally designing an epitope-protein scaffold to elicit selected neutralizing antibodies. Removing from consideration the second biological structures which exhibit a binding energy with the third biological structure which is less than a first selected threshold. Removing from consideration the second biological structures which demonstrate a steric repulsion greater than a selected amount between at least one of the third biological structures and the first biological structure after the first biological structure is positioned within the portion of the second biological structure and Positioning the first biological structure within the portion of the second biological structure to create a combination of the first and second biological structures Identifying at least a portion of the second biological structure which is a geometric match to the first biological structure Selecting at least a portion of first biological structure Obtaining a geometry of at least one of a first biological structure which is recognized by an immune system, a second biological structure which allows interaction between other biological molecules, and a third biological structure which forms a portion of the immune system capable of recognizing the first biological structure In an embodiment, a method of computationally designing a biological structure which evokes a selected immune response is provided. Vaccines to date, while generating high antibody titers, fail to produce a response from one or more of the neutralizing antibodies.įrom the foregoing, then, there exists a need for new immunization strategies for pathogens which have proven resistant to conventional approaches. For example, there are a variety of broadly neutralizing anti-HIV antibodies known to target gp41, including, but are not limited to, 2F5, 2G12, B12, 4E10, and Z13. Some strategies for developing vaccines for HIV have focused on eliciting antibodies directed towards gp120 or gp41. This glycoprotein complex enables HIV to attach to and fuse with target cells to initiate the infectious cycle. The HIV protein comprises a cap made of glycoprotein 120 (gp120) and a stem made from glycoprotein 41 (gp41) which anchors the cap to the HIV protein to the viral envelope. In general, HIV is roughly spherical viral envelope, through which the HIV protein protrudes. In the case of certain pathogens, for example HIV, successful immunization strategies have yet to be realized. Thus, administration of an antigenic composition, a vaccine, can provide controlled exposure to an antigen, allowing the body to protect itself from the antigen later in life and providing a degree of immunity. For example, after the human immune system is exposed to an antigen once, the system can quickly develop a response to subsequent infection. The organism is exposed to an agent that stimulates an immune response, an antigen, in order to fortify the organism's immune system against that agent. Immunizations are designed to take advantage of the immune response of an organism. The tip region of the antibody precisely fits with the epitope region of the antigen, allowing the antibody to target only its corresponding epitope, providing the antibody with high specificity. The region upon the antigen that is recognized by the antibody is referred to as an epitope. Each of these variants can bind to different targets, referred to as antigens, allowing the antibody to recognize an equally wide variety of antigens. While the structure of various antibodies is similar, generally “Y” shaped, a tip region at the surface of the branched arms is highly variable. Antibodies are a part of the immune system response found within the blood which performs the identification and neutralizing functions. The immune system is a collection of mechanisms within an organism which protects the organism from infections by acting to identify and neutralize disease causing biological agents. BACKGROUND OF THE INVENTIONĮmbodiments of the present disclosure relate to immunization and, in particular, to algorithms for facilitating the transplant of selected epitopes recognized by selected antibodies into an appropriate scaffold, while preserving structure and antigenicity and the resultant epitope-scaffold systems. 25, 2006, which is hereby incorporated by reference in its entirety. This application claims the benefit of U.S.
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