###################################################################################################### ### ### ### Blueprint file for building backbone of the former half of a ferredoxin-like fold structure. ### ### This file is used for specifying secondary structure strings. ### ### ### ### Principles for designing ideal protein structures ### ### Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, Rong Xiao, Thomas B. Acton, ### ### Gaetano T. Montelione, and David Baker ### ### Nature 2012, Supplementary Data ### ### ### ###################################################################################################### # # (The lines started with '#' are comments.) # ## SSPAIR is strand-pairs information for the constraints between strands. SSPAIR 1-3.A.0;2-3.A.0 # # SSPAIR is expressed in the following style, # # (strand-id)-(strand-id).(P/A).(register_shift);(strand-id)-(strand-id).(P/A).(register_shift);... # # Examples: # 1-2.A.0;1-3.P.-1 means 1st and 2nd strands make anti parallel strand-pair with register shift 0, and # 1st and 3rd strands make parallel strand-pair with register shift -1. # # Examples of a strand pair: # 1-2.P.0 (1st and 2nd strands make parallel strand pair with register shift 0) # 1 ====> 1 ====> 1 =======> # 2 ====> 2 ======> 2 ===> # # 1-2.P.2 (1st and 2nd strands make parallel strand pair with register shift 2) # 1 =====> 1 ====> 1 ========> # 2 ====> 2 ======> 2 ====> # # 1-2.P.-1 (1st and 2nd strands make parallel strand pair with register shift -1) # 1 ====> 1 =====> 1 ========> # 2 ====> 2 ==========> 2 ====> # # 1-2.A.2 (1st and 2nd strands make anti parallel strand pair with register shift 2) # 1 ====> 1 ======> 1 ===========> # 2 <==== 2 <========== 2 <==== # # 1-2.A.-2 (1st and 2nd strands make anti parallel strand pair with register shift -2) # 1 ====> 1 ==========> 1 =====> # 2 <==== 2 <===== 2 <=========== # #################################################################################################### # Secondary structure strings for building backbone: # 1st column: Residue number. The residue positions marked with 0 are newly generated based on a input pdb. # 2nd column: Amino acid type. This is used for the vdw radius of the pseudo side-chain, since there are no amino-acid-dependent score terms. # 3rd column: Secondary structure type, L:loop, E:strand, and H:helix. # 4th column: Build instruction, R:build the assigned positions, and '.':leave the assigned positions as intact. # # 1 V L R 2 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V L R 0 V L R 0 V L R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V H R 0 V L R 0 V L R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V L R 0 V L R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V E R 0 V L R