(PS)2v2: Protein Structure Prediction Server

Molecular Bioinformatics Center

National Chiao Tung University

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CASP8

Sample output

^New(PS)² version 3.0

(PS)²-v2: Protein Structure Prediction Server

CASP8 predictions

Figure 4. Comparison of the (PS)²-v2 server with 45 servers participating in the CASP8 competition for the template selection on 154 TBM targets. The best templates are directly summarized from the CASP8 website (http://predictioncenter.org/casp8/).

Table 1. The performances of the different versions of (PS)² server for 154 TBM targets

CASP8 targets	Best templates in CASP8				(PS)²-original		(PS)²-CASP8		(PS)²-v2
CASP8 targets	Templates	LGA_S	RMSD	Identity	Templates	GDT_TS	Templates	GDT_TS	Templates	GDT_TS
T0388-D1	2p31A	92.16	0.93	56.5	2p31A	90.5	2p31A	90.6	2p31A	90.6
T0389-D1	2oucA	83.87	1.96	30.7	1hzmA	36.6	2oucA	67.2	2oucA	67.2
T0390-D1	1shxB	93.59	1.36	52.1	1shxA	90.5	1shxA	90.3	1shxA	90.3
T0391-D1	1z01_F	72.34	1.89	18.3	1z01A	61.5	2e4qA	57.4	2e4qA	57.4
T0392-D1	1vaeA	93.88	1.56	84.2	1vaeA	87.5	1vaeA	87.5	1vaeA	87.5
T0393-D1	2f1kA	84.24	2.00	18.3	1teaA	63.2	2h78A	59.3	2h78A	59.3
T0393-D2	2i76A	89.17	1.97	24.2	1teaA	35.1	2h78A	31.6	2h78A	31.6
T0394-D1	1h2eA	74.08	1.67	26.1	1xq9A	51.1	1xq9A	51.7	1xq9A	51.7
T0395-D1	1surA	57.48	2.03	17.5	2oq2C	36.4	1zunA	49.1	1zunA	49.1
T0396-D1	1jraA	93.11	1.33	24.2	1oqcA	86.0	1oqcA	86.0	1oqcA	86.0
T0397-D2	2yu9B	89.00	1.99	8.8	1w9iA	18.0	1wltA	26.1	1wltA	26.1
T0398-D1	2rirG	99.12	0.67	58.0	2rirE	94.1	2rirE	94.1	2rirE	94.1
T0398-D2	2rirE	99.57	0.63	66.0	2rirE	98.6	2rirE	98.6	2rirE	98.6
T0399-D1	1s0wC	54.95	2.59	16.7	2g2uB	40.4	2g2uB	42.6	2g2uB	42.6
T0400-D1	2q7bA	94.01	1.32	33.3	2q7bA	85.2	2q7bA	90.5	2q7bA	90.5
T0401-D1	2prvB	67.58	2.18	21.1	2icgA	54.5	2prvA	61.8	2prvA	61.8
T0402-D1	1rfeA	91.20	1.62	18.8	2i02A	82.2	2i02A	81.4	2i02A	81.4
T0404-D1	2cz4C	96.18	0.98	28.2	2cz4A	93.0	2cz4A	92.7	2cz4A	92.7
T0406-D1	2ou6A	69.82	1.96	13.3	2f22B	51.0	2hkvA	62.9	2hkvA	62.9
T0407-D1	2anuC	57.38	2.27	22.8	2hnhA	34.1	2anuA	62.6	2anuA	62.6
T0407-D2	1z9oA	59.11	2.38	10.0	2hnhA	16.5	2anuA	-	2iakB	17.8
T0408-D1	2af7F	85.74	2.12	19.6	2af7D	79.8	1vkeE	63.5	2af7D	75.3
T0409-D1	2vnuD	83.76	1.55	12.7	1wv3A	29.4	1bkbA	75.4	1bkbA	77.8
T0411-D1	1e0cA	80.10	1.85	22.3	1uarA	66.1	2hhgA	74.4	2hhgA	74.4
T0412-D1	2o0yB	83.71	1.66	18.2	1mkmB	61.2	2o99C	73.3	2o99C	73.3
T0413-D1	1jjiD	44.05	2.40	15.3	2ecfA	32.9	1jjfA	35.7	1jjfA	35.7
T0414-D1	2b5hA	71.97	1.96	7.8	1fi2A	44.7	2pa7A	50.0	2pa7A	50.0
T0415-D1	3bs1A	78.21	1.79	21.5	3bs1A	72.9	3bs1A	74.5	3bs1A	75.0
T0416-D1	2qgnA	93.82	1.39	46.8	2qgnA	69.0	2qgnA	86.0	2qgnA	86.0
T0417-D1	2cnmC	77.10	2.00	14.7	2j8mA	55.4	2cntA	65.9	2cntA	65.9
T0418-D1	2hszB	91.88	1.46	26.1	2nyvA	85.6	2pibA	82.3	2hi0A	86.0
T0418-D2	2ah5A	90.49	1.38	24.2	2nyvA	76.1	2pibA	69.6	2hi0A	72.8
T0419-D1	1e98A	47.09	2.42	14.7	4tmkA	26.5	2jaqA	38.1	2jaqA	38.1
T0419-D2	2plrA	45.58	2.44	12.1	4tmkA	5.0	2jaqA	-	2jaqA	36.6
T0420-D1	1hv9B	81.14	1.94	17.3	2v0hA	53.6	1e5kA	56.8	1fxjA	66.4
T0421-D1	2plrA	47.12	2.29	19.8	4tmkA	25.0	2jaqA	40.4	2jaqA	40.4
T0422-D1	3b9pA	85.21	1.40	57.2	3b9pA	79.6	3b9pA	78.3	3b9pA	78.3
T0422-D2	2qpaB	92.77	1.53	21.5	3b9pA	86.9	3b9pA	86.9	3b9pA	86.9
T0423-D1	2otmC	93.38	1.13	32.4	2otmB	91.5	2otmB	91.2	2otmB	91.2
T0424-D1	3cddD	88.63	1.67	21.4	1wruA	76.1	3cddD	78.0	3cddD	78.0
T0424-D2	1wruA	88.60	1.81	25.6	1wruA	75.9	3cddD	78.6	3cddD	78.6
T0424-D3	3cddF	90.69	1.66	19.6	1wruA	78.5	3cddD	79.8	3cddD	79.8
T0425-D1	1jwqA	83.03	1.97	24.3	1jwqA	60.3	1jwqA	64.0	1jwqA	64.0
T0426-D1	2fw4A	98.82	0.77	60.3	1lugA	94.8	2nmxA	96.4	2nmxA	96.4
T0427-D1	1ppjA	74.81	1.93	14.4	1kb9A	54.7	1hr6D	69.5	1hr6D	69.5
T0427-D2	1hr7C	80.35	1.96	15.7	1kb9A	56.9	1hr6D	63.2	1hr6A	63.2
T0428-D1	1xq9B	98.72	0.78	63.8	1xq9A	95.6	1xq9A	95.6	1xq9A	95.6
T0429-D1	2f5kB	92.93	1.23	22.6	2hfvA	15.0	1oh4A	23.6	1oh4A	23.6
T0429-D2	2d9tA	68.77	1.80	10.2	2hfvA	21.3	1oh4A	28.3	1oh4A	28.3
T0430-D1	1zwsB	55.73	1.88	22.4	1unlA	38.2	1unlA	27.7	2r3iA	36.4
T0430-D2	2bheA	50.17	2.05	22.9	1unlA	35.3	1unlA	41.1	2r3iA	35.1
T0431-D1	2iagB	86.97	1.53	32.3	3b6hB	79.0	3b6hB	73.0	3b6hB	73.0
T0431-D2	2iagA	88.74	1.56	33.1	3b6hB	80.0	3b6hB	75.2	3b6hB	75.2
T0432-D1	2dkwA	86.85	1.59	66.9	2dkwA	81.3	2dkwA	81.0	2dkwA	81.0
T0433-D1	1ybvA	91.92	1.65	21.6	1q7bA	69.7	1q7bA	76.8	1q7bA	76.8
T0434-D1	1mvhA	63.75	2.17	23.4	2o8jB	52.2	2rfiA	58.4	2qpwA	63.4
T0435-D1	2qpwA	85.60	1.57	32.4	2qpwA	80.3	2qpwA	79.7	2qpwA	79.7
T0436-D1	1vp4B	59.20	2.23	19.2	1x0mA	60.4	2dtvA	59.3	2dtvA	59.3
T0437-D1	2jz5A	91.26	1.82	33.9	2jz5A	84.6	2jz5A	84.9	2jz5A	84.9
T0438-D1	2oasA	90.65	1.44	29.8	2oasA	86.0	2oasA	87.8	2oasA	87.8
T0438-D2	2oasA	97.21	1.06	49.8	2oasA	93.0	2oasA	92.7	2oasA	92.7
T0440-D1	2yz5A	79.69	1.64	26.6	2yxoB	69.5	2yxoB	71.6	2yxoB	71.6
T0441-D1	2driA	89.00	1.78	17.2	1jftA	73.6	1jftA	73.4	1jftA	73.4
T0441-D2	1sxgA	93.02	1.24	24.7	1jftA	80.8	1jftA	80.5	1jftA	80.5
T0442-D1	2pifB	92.19	1.51	79.4	2pifB	93.8	2pifB	93.8	2pifB	93.8
T0442-D2	2pifB	92.19	1.51	69.9	2pifB	95.9	2pifB	95.9	2pifB	95.9
T0443-D1	2aplA	68.10	2.54	11.9	1ps1A	36.4	1tffA	33.0	1tffA	33.0
T0443-D3	1onvA	68.03	1.74	7.0	1ps1A	30.3	1tffA	-	1p0zA	42.4
T0444-D1	1jk0A	98.00	0.87	66.3	1h0oA	88.1	1h0oA	87.5	1h0oA	87.5
T0445-D1	2hf2B	93.92	1.32	29.4	2hf2B	85.8	2hf2B	87.9	2hf2B	87.9
T0445-D2	1nf2C	85.13	1.99	9.7	2hf2B	62.2	2hf2B	66.6	2hf2B	66.6
T0446-D1	3b77F	86.67	1.95	18.2	3b77A	67.5	3b77A	71.9	3b77A	71.9
T0446-D2	2j0kA	91.23	1.72	16.3	3b77A	68.5	3b77A	67.0	3b77A	67.0
T0447-D1	1eg7A	95.15	1.12	52.3	1eg7A	88.8	1eg7A	88.6	1eg7A	88.6
T0448-D1	3bzwE	89.15	1.57	26.0	3bzwA	75.4	3bzwA	76.2	3bzwA	76.2
T0449-D1	2cisA	62.10	1.80	21.5	1nsxB	42.6	1lurA	54.5	1snzA	55.2
T0450-D1	2rghA	91.31	1.41	42.2	2rghA	84.0	2rghA	79.3	2rghA	79.3
T0451-D1	1s5aD	84.14	1.87	20.8	1s5aB	65.2	1s5aB	67.1	1tuhA	68.9
T0452-D1	3c8mA	89.16	1.83	29.6	2ejwA	65.2	2ejwA	77.7	2ejwA	77.7
T0452-D2	2ejwA	93.68	1.30	42.5	2ejwA	88.3	2ejwA	89.6	2ejwA	89.6
T0453-D1	2plsI	91.42	1.66	38.8	2plsA	83.4	2plsA	83.4	2plsA	83.4
T0454-D1	2jj7A	97.76	0.98	36.5	2iaiA	82.2	1pb6A	91.8	1pb6A	91.8
T0454-D2	1vi0B	75.11	2.16	10.2	2ibdA	64.1	1pb6A	59.3	1pb6A	59.3
T0455-D1	3bwgB	93.16	1.59	25.2	2ooiB	78.6	3bwgB	86.3	3bwgB	86.3
T0456-D1	2gs7B	88.75	1.67	22.6	2qg5A	75.9	2qg5A	75.6	2qg5A	75.6
T0456-D2	2qg5B	90.02	1.20	44.4	2qg5A	78.7	2qg5A	79.4	2qg5A	79.4
T0457-D1	1wpmB	63.49	2.30	16.7	1ir6A	41.9	1k20A	58.0	1k20A	60.6
T0457-D2	1ir6A	59.63	2.55	12.5	1ir6A	37.9	1k20A	37.5	1k20A	45.8
T0458-D1	2okaA	99.39	0.71	55.8	2okaA	96.1	2fa8B	95.8	2fa8B	95.8
T0459-D1	1yyvA	91.67	1.56	25.8	2f2eA	75.3	1z7uA	76.7	1z7uA	76.7
T0460-D1	2fug5	56.59	2.51	16.7	2h2wA	-	2pr5A	23.1	1q33A	32.2
T0461-D1	2b3jB	89.90	1.32	31.5	2nx8A	83.1	2nx8A	84.7	2nx8A	84.7
T0462-D1	2gcxA	82.80	2.05	33.3	2gcxA	72.1	2gcxA	71.1	2gcxA	71.1
T0462-D2	2gcxA	76.93	2.17	17.2	2gcxA	75.3	2gcxA	77.4	2gcxA	77.4
T0463-D1	1he3A	81.59	1.94	23.3	2c29F	60.3	1r6dA	56.9	1r6dA	58.6
T0464-D1	1b6bA	50.32	2.62	5.6	2jnyA	42.0	2pk7A	46.4	2pk7A	46.4
T0466-D1	1xjvA	74.89	1.94	1.6	1ogoX	21.2	1xq4A	32.3	1xq4A	32.3
T0468-D1	2oq0C	66.59	2.54	11.5	1gsoA	27.0	1bbpA	26.6	1bbpA	28.3
T0469-D1	2fi0A	79.54	2.17	23.0	2fi0A	75.8	2fi0A	75.8	2fi0A	75.8
T0470-D1	2qgsA	92.19	1.92	35.1	2pjqB	79.3	2qgsA	85.6	2qgsA	85.6
T0470-D2	2qgsB	96.54	1.19	49.3	2pjqB	87.7	2qgsA	94.5	2qgsA	94.5
T0471-D1	2r3sA	84.88	1.99	10.6	2absA	24.4	2nwrA	32.7	1nv8A	61.7
T0472-D1	1uwbA	88.70	1.99	15.5	3bidE	73.7	3bidE	74.6	3bidE	74.6
T0472-D2	3bidE	90.99	1.34	18.6	3bidE	86.7	3bidE	86.7	3bidE	86.7
T0473-D1	2fi0A	82.34	2.19	21.1	2fi0A	75.8	2fi0A	75.4	2fi0A	74.2
T0474-D1	2ay0C	97.88	0.94	12.2	1vr6A	37.2	1fadA	51.2	2cpgB	78.7
T0475-D1	1qjgF	89.44	1.80	22.4	1ohpA	75.4	1ohpA	75.6	1ohpA	79.2
T0476-D1	2zbzA	46.85	2.84	12.5	2gx9A	23.3	2c5kT	22.7	2c5kT	23.9
T0477-D1	2db3A	82.43	1.81	32.6	2db3A	75.1	2db3A	76.5	2db3A	76.0
T0478-D1	1xlyA	70.28	2.50	8.6	1toaA	26.8	2v0oA	35.1	1h6gA	42.1
T0478-D2	1xlyB	68.69	2.29	9.5	1toaA	9.6	2v0oA	29.8	1h6gA	38.1
T0479-D1	1zkiB	95.23	1.21	29.2	1zkiA	89.1	1zkiA	88.9	1zkiA	90.4
T0480-D1	1dl6A	89.62	1.74	23.3	3cngC	60.8	2zkr2	59.2	2zkr2	59.2
T0481-D1	1rxqA	67.20	2.21	14.5	2f22B	64.1	2hkvA	64.1	2hkvA	64.1
T0483-D1	1xr1A	84.10	1.81	31.5	2qnjB	64.1	2qnjB	62.7	2qnjB	62.7
T0485-D1	2o57C	70.41	2.19	20.6	3busA	59.3	1im8A	58.9	1im8A	58.9
T0486-D1	2vssF	92.29	1.55	24.8	2hw5A	80.0	2pbpA	80.4	2pbpA	80.4
T0487-D1	2f8sB	62.09	2.14	18.8	1yvuA	59.7	2f8sA	62.9	2f8sA	62.9
T0487-D2	2f8sB	49.37	2.71	13.6	1yvuA	45.3	2f8sA	35.3	2f8sA	35.3
T0487-D3	2f8sB	67.56	2.22	7.6	1yvuA	47.5	2f8sA	65.1	2f8sA	65.1
T0487-D4	1si2A	72.02	2.34	12.2	1yvuA	50.3	2f8sA	37.4	2f8sA	37.4
T0487-D5	1w9hA	54.94	2.65	14.7	1yvuA	51.0	2f8sA	51.9	2f8sA	51.9
T0488-D1	2qg1A	95.98	1.08	35.3	2he2A	84.3	2qg1A	92.7	2qg1A	92.7
T0489-D1	1zxvA	38.36	2.70	10.4	1ei9A	11.3	1jq5A	13.6	1jq5A	13.6
T0490-D1	1ryiA	72.44	2.04	16.8	2qcuB	60.6	1y56B	68.8	1y56B	68.8
T0491-D1	1wocD	92.40	1.49	27.7	1wocC	82.6	1wocC	81.8	1wocC	82.8
T0492-D1	2gcxA	81.58	2.00	24.6	2gcxA	71.0	2h3jA	71.7	2h3jA	71.7
T0493-D1	2is4A	89.58	1.85	23.5	2is6A	36.2	1pjrA	74.0	1pjrA	74.0
T0494-D1	2eu9A	82.74	1.56	32.7	2eu9A	74.1	2eu9A	72.5	2eu9A	72.5
T0495-D1	2okfB	46.66	2.47	11.2	1y0kA	11.2	1gefA	37.6	1gefA	37.6
T0496-D2	3bvoB	99.13	0.78	13.3	1pp9A	55.0	2pbrA	37.2	1dd5A	71.1
T0497-D1	2qeaA	88.52	2.00	29.8	2qeaA	75.2	2i02A	74.6	2i02A	74.6
T0498-D1	2fs1A	94.64	1.22	62.2	1pgxA	37.8	2qmtA	36.7	2qmtA	36.7
T0499-D1	1qkzA	93.48	1.40	60.7	1pgxA	83.0	1pgxA	83.0	1pgxA	83.0
T0501-D1	1wpnB	57.16	2.29	17.0	1i74A	56.9	1k20A	58.9	1k20A	58.9
T0501-D2	1ir6A	62.17	2.36	11.9	1i74A	31.9	1k20A	55.4	1k20A	55.4
T0502-D1	2k50A	87.64	1.68	27.5	1ynxA	68.0	1o7iA	73.1	1o7iA	73.1
T0503-D1	1o3rA	75.86	2.06	16.7	2h6bA	54.9	1hw5A	66.0	1hw5A	66.0
T0504-D1	2f5kA	86.16	1.27	7.3	2g3rA	17.3	2ns2A	44.4	2g3rA	74.2
T0504-D2	2hqeA	62.17	2.11	14.3	2g3rA	48.9	2ns2A	25.6	2g3rA	32.2
T0504-D3	2r5aA	95.44	1.42	17.0	2g3rA	56.1	2ns2A	41.0	2eqmA	80.7
T0505-D1	1rkqA	92.85	1.29	35.7	1rkqA	89.0	1rkqA	89.5	1rkqA	89.5
T0505-D2	2hf2B	68.76	1.96	5.5	1rkqA	61.3	1rkqA	63.0	1rkqA	63.0
T0506-D1	2arzA	92.07	1.48	23.1	2arzA	84.5	2arzA	80.8	2arzA	80.8
T0506-D2	2arzA	88.29	2.10	22.1	2arzA	77.2	2arzA	79.8	2arzA	79.8
T0507-D1	2pidB	70.71	2.12	9.5	1od6A	33.7	1cozA	59.9	1cozA	62.1
T0508-D1	1eizA	91.97	1.42	32.0	1ej0A	84.2	1ej0A	84.5	1ej0A	84.5
T0509-D1	2hnkB	86.77	1.88	20.5	2avdA	72.7	2hnkB	76.9	2hnkB	76.9
T0510-D1	1r2zA	50.37	2.04	4.7	1tdzA	14.7	1tdzA	16.6	1tdzA	24.5
T0510-D2	2f5sA	73.33	2.29	18.2	1tdzA	48.5	1tdzA	51.8	1tdzA	67.3
T0511-D1	1vl8B	82.09	1.70	25.0	2uvdA	71.4	2uvdA	70.0	2uvdA	70.0
T0512-D1	1l0qB	65.73	2.12	18.8	1l0qA	55.6	1l0qA	62.0	1l0qA	62.0
T0513-D1	2fkbA	64.85	2.06	14.7	1vk6A	30.2	2fkbC	48.7	2fkbC	48.7
T0514-D1	2zf8A	47.10	2.70	8.0	1t1gA	12.3	1ogaD	14.8	1ikpA	17.5
Sum of GDT_TS scores					9447.5		9954.4		10331.4

Contact

Chen CC, Hwang JK, Yang JM. (PS)²: protein structure prediction server. NAR 2006, 34, W152-W157
Chen CC, Hwang JK, Yang JM: (PS)²-v2: template-based protein structure prediction server. BMC Bioinformatics 2009, 10:366