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Pipeline publication

[…] b'the structural matching of the 3D models with other known proteins it inferred function of the protein and the output contains full-length secondary and tertiary structure predictions, and functional annotations on ligand-binding sites, Enzyme Commission numbers and Gene Ontology terms in the results (Roy et al. ). Since the unavailability of proper prediction, we used the COACH (Yang et al. ) for protein\xe2\x80\x93ligand-binding site prediction and COFACTOR (Roy et al. ) for structure-based biological function annotation of HP, for proper function analysis of P44095., Predicted models were further refined using a side-chain refinement protocol of Discovery Studio 3.5, which uses force fields such as CHARMM (Brooks et al. ) and SCWRL4 (Krivov et al. ), and predicts positions of the side chains which are used for refinement of predicted protein structures. The final models were further validated by PROCHECK suite (Laskowski et al. ), a module of SAVES (Structural Analysis and Verification Server)., Three-dimensional structure of homologous proteins often remains more conserved than their sequence (Chothia and Lesk ). Structural similarities are more reliable than that of sequences for grouping together distant homologues (Taylor and Orengo ). Three-dimensional structure of all models was analyzed by various servers for function prediction. Identifying the functional region of protein is an important step towards characterizing its molecular function. We used POCASA (Yu et al. ), Pocket-Finder (Laurie and Jackson ) and firestar server (Lopez et al. ) for prediction of functionally impor' […]

Pipeline specifications

Software tools CHARMM, SCWRL, PROCHECK