Biomedical Innovations Research for Translational Health Science (BIRTHS) Laboratory, Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila, Philippines.
Methods Mol Biol. 2024;2821:9-32. doi: 10.1007/978-1-0716-3914-6_2.
B-cell epitope prediction is key to developing peptide-based vaccines and immunodiagnostics along with antibodies for prophylactic, therapeutic and/or diagnostic use. This entails estimating paratope binding affinity for variable-length peptidic sequences subject to constraints on both paratope accessibility and antigen conformational flexibility, as described herein for the HAPTIC2/HEPTAD User Toolkit (HUT). HUT comprises the Heuristic Affinity Prediction Tool for Immune Complexes 2 (HAPTIC2), the HAPTIC2-like Epitope Prediction Tool for Antigen with Disulfide (HEPTAD) and the HAPTIC2/HEPTAD Input Preprocessor (HIP). HIP enables tagging of residues (e.g., in hydrophobic blobs, ordered regions and glycosylation motifs) for exclusion from downstream analyses by HAPTIC2 and HEPTAD. HAPTIC2 estimates paratope binding affinity for disulfide-free disordered peptidic antigens (by analogy between flexible-ligand docking and protein folding), from terms attributed to compaction (in view of sequence length, charge and temperature-dependent polyproline-II helical propensity), collapse (disfavored by residue bulkiness) and contact (with glycine and proline regarded as polar residues that hydrogen bond with paratopes). HEPTAD analyzes antigen sequences that each contain two cysteine residues for which the impact of disulfide pairing is estimated as a correction to the free-energy penalty of compaction. All of HUT is freely accessible online ( https://freeshell.de/~badong/hut.htm ).
B 细胞表位预测是开发基于肽的疫苗和免疫诊断试剂以及用于预防、治疗和/或诊断的抗体的关键。这需要估计可变长度肽序列的变构结合亲和力，同时考虑变构体可及性和抗原构象灵活性的限制，如本文所述，用于 HAPTIC2/HEPTAD 用户工具包 (HUT)。HUT 包括免疫复合物 2 的启发式亲和力预测工具 (HAPTIC2)、具有二硫键的抗原的 HAPTIC2 样表位预测工具 (HEPTAD) 和 HAPTIC2/HEPTAD 输入预处理程序 (HIP)。HIP 能够标记残基 (例如，在疏水区、有序区和糖基化模体中)，以便通过 HAPTIC2 和 HEPTAD 排除在下游分析之外。HAPTIC2 通过将柔性配体对接与蛋白质折叠进行类比，估计无二硫键的无序肽抗原的变构结合亲和力(根据序列长度、电荷和温度依赖性的多脯氨酸-II 螺旋倾向、折叠(由于残基体积较大而不受青睐)和接触(甘氨酸和脯氨酸被视为与变构体形成氢键的极性残基)。HEPTAD 分析每个包含两个半胱氨酸残基的抗原序列，估计二硫键配对的影响作为对紧凑自由能罚分的修正。HUT 全部免费在线提供 (https://freeshell.de/~badong/hut.htm)。
