系列:
rosetta-Model_miss_loop
目的:
补全蛋白结构中缺失的loop
原理:
见参考1,2
步骤:
1:pymol打开任意蛋白
2:删掉其中的一段loop,删掉的是35D,36D,37R
序列:
>original_pdb.pdb 47 bp
GDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHIS
3:是pymol build模块重新建立loop
4:rosetta处理蛋白重新编号
score_jd2.static.linuxgccrelease -in:file:s original_pdb.pdb -renumber_pdb true -out:pdb -out:file renumber.pdb -overwrite
输出文件:original_pdb_0001.pdb
5:设置loop file
#miss_loop.file
LOOP 21 23 21 0 0
解释:
column1 "LOOP": Literally the string LOOP, identifying this line as a loop
In the future loop specification files may take other data.
column2 "integer": Loop start residue number
column3 "integer": Loop end residue number
column4 "integer": Cut point residue number, >=startRes, <=endRes.
column5 "float": Skip rate. default - never skip (0)
column6 "boolean": Extend loop. Set to 1
6:运行rosetta loop model
flags文件:
-s original_pdb_0001.pdb
-loops:loop_file miss_loop.file
-loops:remodel perturb_kic
-loops:refine refine_kic
-ex1
-ex2
-nstruct 100
-loops:max_kic_build_attempts 100
-in:file:fullatom
7:pymol align
8:后续分析
暂无
github:https://github.com/luskyqi1995/protein_lucky/tree/master/rosetta/model_missing_loop
参考:
1:https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/loop_modeling/loopmodel
2:https://zhuanlan.zhihu.com/p/76390180
Everyday you must keep something new.