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Antigen Prediction Tool - Gen. Script. 1. Sequence length: The typical length of the peptide antigen for generating anti- peptide antibodies is in the range of 1. Prediction Program Using Neural Networks NN-PRED. Although several strategies have been proposed to secondary structure prediction, most of the methods. A program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral beta-barrel outer membrane protein. BOMP is based on two separate components to recognize integral beta-barrel. Shorter sequence can offer greater specificity, but at the risk of being less likely to be exposed on the native protein. Longer sequences, by contrast, might be slightly less specific, but offer a higher probability of recognizing the native protein. Peptide sequences with length of 1. Hydrophilic, surface- oriented, and flexible: Peptide antigens are produced against epitope sequences which are most likely to be hydrophilic, surface- oriented, and flexible. To do so, we extend existing ensemble b-sheet prediction. All these simulations can be performed on query sequences using our program. While tertiary structure prediction from protein sequences remains a. A method to predict edge strands in beta-sheets from protein. Using the program pdb23 for any beta-sheet named. The program output files are tables (.xls files). Subramani A, Floudas CA (2012) Beta-sheet topology prediction with high precision and recall for beta and mixed alpha/beta proteins. Most naturally occurring proteins in aqueous solutions have their hydrophilic residues on the protein surface and hydrophobic residues buried in the interior. The strategy of optimizing antigen design to choose epitopes with hydrophilic, surface- exposed sequences is based on the fact that antibodies tend to bind to epitopes on the protein surface. Additionally, it has been shown that epitopes have a high degree of mobility, thus flexibility is also taken into consideration. Targeting the N- terminus or C- terminus: Either the C- termini or N- termini are frequently chosen for generating anti- peptide antibodies. The C- termini and N- termini of proteins are often exposed and have a high degree of flexibility making either a good epitope candidate for antibody production. Though the C- termini is usually a good choice, if the target protein is an integral membrane protein and the C- terminus is part of the transmembrane segment, this sequence will be too hydrophobic to be a good candidate. In this type of circumstance, the N- terminus is a better choice. Also, the leader sequence should not be included in the sequence selected for antibody generation. Continuous versus Discontinuous Epitopes: The Optimum. Antigen. Epitope sequences in proteins generally consist of 6- 1. Continuous epitopes consists of a contiguous sequence of amino acids in a protein. Anti- peptide antibodies will bind to continuous epitopes in native protein when the epitope sequence is exposed on the surface of the protein. Discontinuous epitopes consist of sequences of amino acids that are not contiguous but are brought together when the peptide chain folds or by the juxtaposition of two separate polypeptide chains. Anti- peptide antibodies may or may not recognize a discontinuous epitope depending on whether the peptide used has a secondary structure similar to the epitope and/or if the protein epitope has enough continuous sequence for the antibody to bind with a lower affinity. Algorithms: Our peptide antigen design algorithm takes into account hydrophilicity/hydrophobicity, secondary structure, common sequence motifs, and integrates commercially available algorithms to optimize the peptide design. Hydrophilicity/Hydrophobicity Our antigen design tool integrates several well- known strategies for predicting hydrophilicity/hydrophobicity. Hydrophilicity plots as described by Hopp and Woods assign an average hydrophilicity value for each residue in the sequence and the highest point of average hydrophilicity for a series of contiguous residues is usually at or near an antigenic determinant. A slightly different algorithm described by Kyte and Doolittle evaluates the hydrophilic and hydrophobic tendencies of the sequence. This profile is useful for predicting exterior versus interior regions of the native protein. Secondary Structure Secondary structure can be identified by the algorithms developed by Chou and Fasman or Lim. Knowledge of structure regions including alpha- helix, beta- sheet and beta- turn aids the selection process of a potentially exposed, immunogenic internal sequence for antibody generation. Surface region or regions of high accessibility often border helical or extended secondary structure regions. In addition, sequence regions with beta- turn or amphipthic helix character have been found to be antigenic. Sequence Motifs We avoid common sequence motifs such as the RGD motif, the helix- loop- helix sequence, GTP binding sites, and SH2 domains which may cause cross- reactivity. We also avoid sequences associated with certain biological activities, such as autolytic cleavage hormonal activity, and undesired post- translational modifications. Integration of multiple algorithms We incorporate many commercial software packages such as Mac. Vector. Combined use of several predictive methods may result in a success rate as high as 8. Epitope Analysis and Coupling Strategy: Conjugation chemistries that best mimic epitope presentation are carefully selected. Peptides alone are usually too small to elicit an immune response sufficient to generate antibodies. This is why peptides of interest are conjugated to carrier proteins containing many epitopes that stimulate T- helper cells. These T- cells induce the B- cell response which generates the antibodies. Some of these antibodies will target the linker region and the carrier protein itself in addition to the peptide of interest. These non- specific antibodies can be removed during the purification or screening process. Specificallly, our coupling strategy maximizes epitope exposure within structural motifs and optimizes orientation to the termini. Are Employee Purchase Programs with Payroll Deductions a Good Idea? It sounds like a good plan: Offer your current and retired employees discounts on products and services from companies that you have existing business relationships with. Then, arrange for employees to have payroll deductions to help them more easily pay for these items (without finance charges, of course). These types of employee purchase programs are quite active in some companies, giving employees a semi- personalized . There is certainly some value for both the company (bringing business to their client helps the client be more successful) and the employee (discounts and payroll deduction make payment much easier) with this arrangement. Non-active employees: must be receiving GM pension or healthcare plan. Surviving spouses: must be receiving. Vehicle Purchase Programs Rules and Guidelines. Sponsored Purchasers Eligible Participants are able to sponsor. Did you know that many CHESS contractors offer Government Employee Purchase Programs? With Dell's Price Match Guarantee and Member Purchase Program it's easy to find great deals. EmployeePurchasing.com by McGrath Affinity is focused on analyzing the top Employee Purchasing Programs on the market today. Employee Purchasing Programs are the fastest growing program in benefits today. This benefit also gives employers an extremely low or no cost way to deliver direct value to employees by helping them save money on products and services they may be purchasing anyway . Many employees are already underinsured, some perhaps even living paycheck to paycheck, and some people would argue that employees should never buy anything that they can. Are employees ever encouraged to then contribute more to their retirement plans or buy insurance or other items that can help them financially down the road? Would having that option or information change the value of a employee purchase program? With all the discussion recently on the consumer driven healthcare ? Should there be other consumer driven benefit options, including employee purchase programs? Due diligence is a very important part of any benefit product offered to an employee, even these types of non- traditional offers. So why not find a way to integrate them? Given the advances in technology over the last five years, why not educate employees and offer them some valid tools to help improve their financial future? You just saved $1,0. With that savings, you may want to contribute more to your 4. I suggest we work on creating an employee benefits marketplace where all of these different types of benefit components can work together: 1) consumer choice (which automatically brings some personal responsibility) and 2) employer due diligence including the appropriate vetting of programs and the technology platforms they run on. Integrating core and these types of voluntary benefits is the best way to ensure your benefits programs delivers real value to your employees and is truly in their best interest. What do you think? Discount programs » Employee purchase. Welcome to Employee Programs : Employee Programs. Employees and retirees can take advantage of money and time saving discounts from a variety of HP suppliers and partners. 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