Signatures of T cell immunity revealed using sequence similarity with TCRDivER algorithm.

Changes in the T cell receptor (TCR) repertoires have become important markers for monitoring disease or therapy progression. With the rise of immunotherapy usage in cancer, infectious and autoimmune disease, accurate assessment and comparison of the "state" of the TCR repertoire has become paramount. One important driver of change within the repertoire is T cell proliferation following immunisation.

T Cell Epitope Prediction and Its Application to Immunotherapy.

T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for epitope prediction, with a particular focus on tools aimed at identifying neoepitopes, i.e.

T cell receptor sequence clustering and antigen specificity.

There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available.

Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

In this work, we explore the applicability and limitations of the current third order density functional tight binding (DFTB3) formalism for treating transition metal ions using nickel as an example. To be consistent with recent parameterization of DFTB3 for copper, the parametrization for nickel is conducted in a spin-polarized formulation and with orbital-resolved Hubbard parameters and their charge derivatives. The performance of the current parameter set is evaluated based on structural and energetic properties of a set of nickel-containing compounds that involve biologically relevant ligands.

in/out Isomerism of cyclophanes: a theoretical account of 2,6,15-trithia-[3][7]metacyclophane and [3][7]metacyclophane as well as their halogen substituted analogues.

A detailed theoretical investigation of cyclophanes with a divergent set of methods ranging from molecular mechanics through semiempirical to ab initio is presented. Cyclophanes have attracted interest over the years due to their unusual chemistry and increasing applications. There has been previous debate over the effects contributing to the greater stability of more-crowded in isomers of certain cyclophanes, and a higher strain in the out isomer was the prevailing explanation.

A Comparative Study of Chromatographic Behavior and Lipophilicity of Selected Imidazoline Derivatives.

Chromatographic behavior and lipophilicity of 20 selected imidazoline derivatives were examined by thin-layer chromatography using CN, RP-2, RP-8 and RP-18 as the stationary phases and a mixture of methanol, water and ammonia as the mobile phase. In all examined chromatographic systems, linear relationships were established between retention parameters and the volume fraction of methanol in the mobile phase (r > 0.985, 0.