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Table 1 The essential differences of (PS)2-original, (PS)2-CASP8 and (PS)2-v2

From: (PS)2-v2: template-based protein structure prediction server

Steps (PS)2-original[16] (PS)2-CASP8[17] (PS)2-v2
1. Template search Consensus of PSI-BLAST and IMPALA S2A2+PSSM with a self-developed aligned tool using dynamic programming S2A2+PSSM with a modified SSEARCH program [18]
2. Target-template alignment Consensus of PSI-BLAST, IMPALA and T-coffee S2A2+PSSM with a self-developed aligned tool using dynamic programming S2A2+PSSM with a modified SSEARCH program [18]
3. Template Single template Single template Multiple templates
4. Model building MODELLER with single model MODELLER with single model MODELLER with multiple models
5. Model evaluation PROCHECK [42] PROCHECK ProQ [19]