Dr. Jenny J. Yang's Lab

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Calciomics is a specialized area of biochemistry focusing on the study of calcium-binding biological macromolecules and proteins to understand the factors that contribute to calcium-binding affinity and the selectivity of proteins and calcium-dependent conformational change.

CaPS (Calcium Pattern Search) provides a list of Ca(II)-binding AA sequence patterns that indicate the presence of a Ca(II)-binding motif. To date, we have developed sequence patterns, or signatures, for canonical EF-hand, pseudo EF-hand, and bacterial EF-hand. We expect to significantly expand this list in the future to include non-contiguous (binding motif includes AA residues distant from each other in the primary structure) patterns. To check a sequence for the presence of a Ca(II)-binding signature click on the CaPS link and enter your sequence for analysis.

GG is a graph-theoretic and geometric analysis program developed by Hai Deng, Guan Tao Chen, Wei Yang, and Jenny J Yang. The program is used for predicting Ca(II)-binding sites in protein based on the geometric information.

MUG is a prediction algorithm with atomic resolution of calcium-binding sites in proteins. After first identifying all possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca2+ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures.

<Beta Version >MUGC recognizes Ca(2+)-binding sites without explicit reference to side-chain oxygen ligand coordinates. By using second shell carbon atoms, main-chain oxygen atoms, center of mass of side-chain, and graph theory, it is able to predict calcium-binding sites exhibiting insignificant conformational change with high sensitivity and selectivity based on X-ray structures or NMR structures.