The directory contains data for the manuscript "Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals"

Rosetta_models directory contains Abs homology models and corresponding score files.

All other directories contain MD simulation data. Each subdirectory contains Amber restart files (.crd; coordinates and velocities for all solute and solvent atoms) and Amber simulation output files (.out; simulation data, including input information and random seeds).

HEPC3 (straight):

• HEPC3_Fv_crystal_relaxed2
• trial_0/HEPC3_Fv_crystal_relaxed2
• trial_1/HEPC3_Fv_crystal_relaxed2
• trial_2/HEPC3_Fv_crystal_relaxed2
• trial_3/HEPC3_Fv_crystal_relaxed2
• trial_4/HEPC3_Fv_crystal_relaxed2

HEPC3 (bent):

• HEPC3_Fv_bent_cm_relaxed2
• trial_0/HEPC3_Fv_bent_cm_relaxed2
• trial_1/HEPC3_Fv_bent_cm_relaxed2
• trial_2/HEPC3_Fv_bent_cm_relaxed2
• trial_3/HEPC3_Fv_bent_cm_relaxed2
• trial_4/HEPC3_Fv_bent_cm_relaxed2

HEPC3-PG (HEPC3-V97P-N100GG) (straight):

• HEPC3_Fv_crystal_PG_relaxed
• trial_0/HEPC3_Fv_crystal_PG_relaxed
• trial_1/HEPC3_Fv_crystal_PG_relaxed
• trial_2/HEPC3_Fv_crystal_PG_relaxed
• trial_3/HEPC3_Fv_crystal_PG_relaxed
• trial_4/HEPC3_Fv_crystal_PG_relaxed

HEPC3-PG (HEPC3-V97P-N100GG) (bent):

• HEPC3_Fv_bent_cm_PG_relaxed
• trial_0/HEPC3_Fv_bent_cm_PG_relaxed
• trial_1/HEPC3_Fv_bent_cm_PG_relaxed
• trial_2/HEPC3_Fv_bent_cm_PG_relaxed
• trial_3/HEPC3_Fv_bent_cm_PG_relaxed
• trial_4/HEPC3_Fv_bent_cm_PG_relaxed

HEPC3.1 (bent):

• HEPC3-1_Fv_full_relaxed2
• trial_0/HEPC3-1_Fv_full_relaxed2
• trial_1/HEPC3-1_Fv_full_relaxed2
• trial_2/HEPC3-1_Fv_full_relaxed2
• trial_3/HEPC3-1_Fv_full_relaxed2
• trial_4/HEPC3-1_Fv_full_relaxed2

HEPC3.1 (straight):

• HEPC3-1_Fv_straight_cm_relaxed2
• trial_0/HEPC3-1_Fv_straight_cm_relaxed2
• trial_1/HEPC3-1_Fv_straight_cm_relaxed2
• trial_2/HEPC3-1_Fv_straight_cm_relaxed2
• trial_3/HEPC3-1_Fv_straight_cm_relaxed2
• trial_4/HEPC3-1_Fv_straight_cm_relaxed2

HEPC3.1-VN (HEPC3.1-P97V-G100GN) (straight):

• HEPC3-1_Fv_straight_VN_relaxed
• trial_0/HEPC3-1_Fv_straight_VN_relaxed
• trial_1/HEPC3-1_Fv_straight_VN_relaxed
• trial_2/HEPC3-1_Fv_straight_VN_relaxed
• trial_3/HEPC3-1_Fv_straight_VN_relaxed
• trial_4/HEPC3-1_Fv_straight_VN_relaxed

HEPC3.1-VN (HEPC3.1-P97V-G100GN) (bent):

• HEPC3-1_Fv_full_VN_relaxed
• trial_0/HEPC3-1_Fv_full_VN_relaxed
• trial_1/HEPC3-1_Fv_full_VN_relaxed
• trial_2/HEPC3-1_Fv_full_VN_relaxed
• trial_3/HEPC3-1_Fv_full_VN_relaxed
• trial_4/HEPC3-1_Fv_full_VN_relaxed

HEPC3.4 (bent):

• HEPC3-4_Fv_full_relaxed2
• trial_0/HEPC3-4_Fv_full_relaxed2
• trial_1/HEPC3-4_Fv_full_relaxed2
• trial_2/HEPC3-4_Fv_full_relaxed2
• trial_3/HEPC3-4_Fv_full_relaxed2
• trial_4/HEPC3-4_Fv_full_relaxed2

HEPC3.4 (straight):

• HEPC3-4_Fv_straight_cm_correct_relaxed2
• trial_0/HEPC3-4_Fv_straight_cm_correct_relaxed2
• trial_1/HEPC3-4_Fv_straight_cm_correct_relaxed2
• trial_2/HEPC3-4_Fv_straight_cm_correct_relaxed2
• trial_3/HEPC3-4_Fv_straight_cm_correct_relaxed2
• trial_4/HEPC3-4_Fv_straight_cm_correct_relaxed2

HEPC3.4-VN (HEPC3.4-P97V-G100GN) (bent):

• HEPC3-4_Fv_full_VN_relaxed
• trial_0/HEPC3-4_Fv_full_VN_relaxed
• trial_1/HEPC3-4_Fv_full_VN_relaxed
• trial_2/HEPC3-4_Fv_full_VN_relaxed
• trial_3/HEPC3-4_Fv_full_VN_relaxed
• trial_4/HEPC3-4_Fv_full_VN_relaxed

HEPC3.4-VN (HEPC3.4-P97V-G100GN) (straight):

• HEPC3-4_Fv_straight_correct_VN_relaxed
• trial_0/HEPC3-4_Fv_straight_correct_VN_relaxed
• trial_1/HEPC3-4_Fv_straight_correct_VN_relaxed
• trial_2/HEPC3-4_Fv_straight_correct_VN_relaxed
• trial_3/HEPC3-4_Fv_straight_correct_VN_relaxed
• trial_4/HEPC3-4_Fv_straight_correct_VN_relaxed