High accuracy semidefinite programming bounds for kissing numbers

The kissing number in n-dimensional Euclidean space is the maximal number of non-overlapping unit spheres which simultaneously can touch a central unit sphere. Bachoc and Vallentin developed a method to find upper bounds for the kissing number based on semidefinite programming. This paper is a report on high accuracy calculations of these upper bounds for n <= 24. The bound for n = 16 implies a conjecture of Conway and Sloane: There is no 16-dimensional periodic point set with average theta series 1 + 7680q^3 + 4320q^4 + 276480q^5 + 61440q^6 + ...Comment: 7 pages (v3) new numerical result in Section 4, to appear in Experiment. Mat

Semidefinite code bounds based on quadruple distances

Let $A(n,d)$ be the maximum number of $0,1$ words of length $n$, any two having Hamming distance at least $d$. We prove $A(20,8)=256$, which implies that the quadruply shortened Golay code is optimal. Moreover, we show $A(18,6)\leq 673$, $A(19,6)\leq 1237$, $A(20,6)\leq 2279$, $A(23,6)\leq 13674$, $A(19,8)\leq 135$, $A(25,8)\leq 5421$, $A(26,8)\leq 9275$, $A(21,10)\leq 47$, $A(22,10)\leq 84$, $A(24,10)\leq 268$, $A(25,10)\leq 466$, $A(26,10)\leq 836$, $A(27,10)\leq 1585$, $A(25,12)\leq 55$, and $A(26,12)\leq 96$. The method is based on the positive semidefiniteness of matrices derived from quadruples of words. This can be put as constraint in a semidefinite program, whose optimum value is an upper bound for $A(n,d)$. The order of the matrices involved is huge. However, the semidefinite program is highly symmetric, by which its feasible region can be restricted to the algebra of matrices invariant under this symmetry. By block diagonalizing this algebra, the order of the matrices will be reduced so as to make the program solvable with semidefinite programming software in the above range of values of $n$ and $d$.Comment: 15 page

Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model

<p>Abstract</p> <p>Background</p> <p>The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous number of possible peptide epitopes prevents their complete experimental characterization. Computational methods can utilize the limited experimental data to predict the binding affinities of peptides to class II MHC.</p> <p>Results</p> <p>We have developed the Regularized Thermodynamic Average, or RTA, method for predicting the affinities of peptides binding to class II MHC. RTA accounts for all possible peptide binding conformations using a thermodynamic average and includes a parameter constraint for regularization to improve accuracy on novel data. RTA was shown to achieve higher accuracy, as measured by AUC, than SMM-align on the same data for all 17 MHC allotypes examined. RTA also gave the highest accuracy on all but three allotypes when compared with results from 9 different prediction methods applied to the same data. In addition, the method correctly predicted the peptide binding register of 17 out of 18 peptide-MHC complexes. Finally, we found that suboptimal peptide binding registers, which are often ignored in other prediction methods, made significant contributions of at least 50% of the total binding energy for approximately 20% of the peptides.</p> <p>Conclusions</p> <p>The RTA method accurately predicts peptide binding affinities to class II MHC and accounts for multiple peptide binding registers while reducing overfitting through regularization. The method has potential applications in vaccine design and in understanding autoimmune disorders. A web server implementing the RTA prediction method is available at <url>http://bordnerlab.org/RTA/</url>.</p

MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes

abstract: Background The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due to MHC diversity and the large number of possible peptide sequences. Computational methods trained on the limited experimental binding data can address this challenge. We present the MultiRTA method, an extension of our previous single-type RTA prediction method, which allows the prediction of peptide binding affinities for multiple MHC allotypes not used to train the model. Thus predictions can be made for many MHC allotypes for which experimental binding data is unavailable. Results We fit MultiRTA models for both HLA-DR and HLA-DP using large experimental binding data sets. The performance in predicting binding affinities for novel MHC allotypes, not in the training set, was tested in two different ways. First, we performed leave-one-allele-out cross-validation, in which predictions are made for one allotype using a model fit to binding data for the remaining MHC allotypes. Comparison of the HLA-DR results with those of two other prediction methods applied to the same data sets showed that MultiRTA achieved performance comparable to NetMHCIIpan and better than the earlier TEPITOPE method. We also directly tested model transferability by making leave-one-allele-out predictions for additional experimentally characterized sets of overlapping peptide epitopes binding to multiple MHC allotypes. In addition, we determined the applicability of prediction methods like MultiRTA to other MHC allotypes by examining the degree of MHC variation accounted for in the training set. An examination of predictions for the promiscuous binding CLIP peptide revealed variations in binding affinity among alleles as well as potentially distinct binding registers for HLA-DR and HLA-DP. Finally, we analyzed the optimal MultiRTA parameters to discover the most important peptide residues for promiscuous and allele-specific binding to HLA-DR and HLA-DP allotypes. Conclusions The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA.The electronic version of this article is the complete one and can be found online at: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-48