Fold Recognition

Profacgen provides our expertise in helping recognize the correct structural fold among known template protein structures for a target protein by combining sequence profile-profile alignment with multiple structural information. Our approach starts with the construction of a structure template database/library, and then incrementally replacing the sequence of a known protein structure in a library with a query sequence of unknown structure. Alignment of the target sequence with each of the structure templates is achieved by optimizing the designed scoring function. The process is repeated against all known 3D structures in the template database until an optimal fit is found. The most statistically probable alignment is selected as the threading prediction and a structural model is constructed for the target by placing the backbone atoms of the target sequence at their aligned backbone positions of the selected structural template. Unlike sequence-only comparison, these methods take advantage of the extra information made available by 3D structure information. The resultant structural models are all quality validated and can be used downstream in silico or experimental work such as protein engineering and drug design.

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