無風的日子: 2014

2014年9月10日星期三

Docking study

0 意見張貼者： Windlessday 於上午8:25

Protein structure : From PDB or Modelling
Ligand structure :

Copy smiles from PDB
[Zinc website] : search --> structure --> paste smiles --> format : SDF --> Run query --> save zine.sdf
copy zine.sdf to iGEMDOCK folder --> run split-zine.exe --> XXX.mol

iGEMDOCK

Prepare binding site --> XXX.pdb
Prepare compounds ---> ***.mol
Start docking

2014年7月21日星期一

Amino acid 特性表

0 意見張貼者： Windlessday 於上午11:46

Feature Category			Ala	Arg	Asn	Asp	Cys	Glu	Gln	Gly	His	Ile	Leu	Lys	Met	Phe	Pro	Ser	Thr	Trp	Tyr	Val
Feature Count	Active or catalytic sites		7	137	71	197	110	120	35	82	225	3	14	94	2	18	10	69	44	4	31	3
	Binding sites		59	247	93	332	128	181	85	282	183	48	73	233	24	75	105	131	77	40	69	31
	Functional loops and regions		27	35	14	96	3	34	52	79	52	26	56	18	3	42	41	38	63	2	29	31
	Interfaces		28	78	37	39	11	30	20	35	9	15	32	46	7	31	26	20	10	10	32	32
	Motifs		133	107	109	376	36	102	32	399	72	57	98	368	14	66	50	155	215	30	77	76
	Other sites		4	14	21	38	56	20	3	29	54	7	8	9	3	6	3	49	15	6	13	7
	Sum		258	618	345	1078	344	487	227	906	595	156	281	768	53	238	235	462	424	92	251	180
Charge			0	+	- / +	-	- / +	-	- / +	0	+	0	0	+	0	0	0	- / +	- / +	0	- / +	0
Abundance (%)			8.84	5.7	4.17	5.39	1.24	6.24	3.82	7.03	2.2	5.95	9.94	5.27	2.37	4	4.71	6.72	5.43	1.21	3	6.77
Hydrophobicity			0.81	0	0.45	0.42	0.72	0.46	0.43	0.77	0.55	1	0.92	0.26	0.81	0.95	0.68	0.6	0.63	0.85	0.71	0.92
Side chain flexibility ( No:none; Re:restricted; Li:Limited; Lo:Low; M0:moderate; Hi:high)			Li	Hi	Mo	Mo	Lo	Hi	Hi	No	Mo	Mo	Mo	Hi	Hi	Mo	Re	Lo	Lo	Mo	Mo	Lo
Potential side chain H-bonds			0	7	5	4	0	4	5	0	3	0	0	3	0	0	0	3	3	1	3	0
Interaction modes		Covalent disulfide bonds					Yes
		Ionic		Yes		Yes		Yes			Yes			Yes
		H-bonds		Yes	Yes	Yes		Yes	Yes		Yes			Yes				Yes	Yes	Yes	Yes
		aromatic stacking									Yes					Yes				Yes	Yes
		van der Waals	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes