Automatic workflow for the classification of local DNA conformations

BMC Bioinformatics

Table 1 Characteristics of the local B-DNA backbone conformations used in the present work

Class ID	Description	N	δ	ϵ	ζ	α+ 1	β+ 1	γ+ 1	δ+ 1	χ	χ+ 1
8	A-DNA	325	83	205	287	294	174	54	83	199	202
13	A-DNA, BI-like χ, χ +1	196	89	201	275	294	162	54	89	244	244
19	A-DNA, α+1/γ+1 crank (t/t)	65	82	195	291	149	194	182	87	204	188
32	BI-to-A, O4'-endo δ+1	266	129	186	264	295	170	52	99	247	233
41	A-to-B, >C3'-endo δ, C2'-endo δ+1	215	90	196	280	299	179	55	142	222	256
50	BI, C1'-exo δ+1	392	129	181	265	300	177	50	123	246	245
54	BI	1942	136	183	259	303	181	44	138	252	259
86	BII variation in complexes	314	140	201	216	314	153	46	140	262	253
96	BII	539	143	245	170	297	141	46	141	271	257
109	BII-to-A, C3'-endo δ+1	20	142	213	181	297	139	52	90	273	207
110	BII-to-A, α+1/γ+1 crank (g+/t), high β+1	9	146	257	186	60	224	196	90	260	200
116	BI, α+1/γ+1 crank (g+/g-)	158	140	194	247	31	197	294	150	253	253
119	BI mismatches, syn/anti	11	144	189	266	303	167	53	138	70	259
121	A-to-B, >C3'-endo δ, anti/syn	19	100	209	278	295	174	54	128	243	67
122	BI mismatches, anti/syn, α+1/γ+1 crank (g+/g-)	8	137	196	225	33	187	295	145	257	70
123	Z-DNA, Y-R	21	147	264	76	66	186	179	95	205	61
124	Z-DNA, R-Y ZI	49	96	242	295	209	231	55	144	63	205
126	Z-DNA, R-Y ZII	18	95	187	63	169	162	44	144	58	213

“Class ID” is the symbolic label of the class. “Description ”is a short annotation of the class. “N” is the number of suites (dinucleotides) with the given class membership. Values of torsions represent the arithmetic means for individual classes. Torsions are defined in Figure 2.

ISSN: 1471-2105