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Received September 25, 2017
Accepted November 20, 2017
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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/bync/3.0) which permits
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Computational screening of potential non-immunoglobulin scaffolds using overlapped conserved residues (OCR)-based fingerprints
Ganapathiraman Munussami
Sriram Sokalingam†
Selvakumar Edwardraja
Jung Rae Kim
Sungwook Chung
Sun-Gu Lee†
Department of Chemical and Biomolecular Engineering, Pusan National University, Busan 46241, Korea
biosriram@gmail.com
Korean Journal of Chemical Engineering, March 2018, 35(3), 717-724(8), 10.1007/s11814-017-0350-4
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Abstract
Cystatins and lipocalins have attracted considerable interest for their potential applications in non-immunoglobulin protein scaffold engineering. In the present study, their potential homologs were screened computationally from non-redundant protein sequence database based on the overlapped conserved residues (OCR)-fingerprints, which can detect the protein family with low sequence identity, such as cystatins and lipocalins. Two types of OCR-fingerprints for each family were designed and showed very high detection efficiency (>90%). The protein sequence database was scanned by the fingerprints, which yielded the hypothetical sequences for cystatins and lipocalins. The hypothetical sequences were validated further based on their sequence motifs and structural models, which allowed an identification of the potential homologs of cystatins and lipocalins.
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Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE, Nat. Protoc., 10, 845 (2015)
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Zhang CX, Freddolino PL, Zhang Y, Nucleic. Acids Res., 45, W291 (2017)
