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Pipeline publication

[…] s, energy minimization (steepest descent algorithm for 500 steps) was performed by tolerance of 1000 kJ/mol Å2 to remove initial steric clashes. The energy minimized systems were treated for 1000 ps equilibration run under pressure and temperature conditions to relax the systems. Finally, MD simulations were run for 15 ns time scale under constant temperature (300 K) and pressure (1 atm). PME (Particle Mesh Ewald) algorithm was used in all calculations to dissect electrostatic interactions. Snapshots were collected throughout the MD simulations of each system and PDBs were generated for 1, 5, 10, 12 and 15 ns intervals to investigate the time-dependent behavior and stability of each system. UCSF Chimera ver. 1.7.0 , PyMol (http://www.pymol.org) and GROMACS tools were used to analyze the stability and behavior of each system., Pilin (PDB ID: 1PAO) was found by screening the consensus DYNLL1 binding motif KSTQT against PDB database. It is a fimbrial protein of gram negative bacteria PAO, a strain of P. aeruginosa and encoded by the pilA gene. We identified that Pilin contains a homologous sequence (KSTQD) to DYNLL1 binding motif in its receptor binding domain (). This motif is present in several DYNLL1-interacting proteins such as human adenovirus protease, BimEL, MAP4, P protein Rabies virus, P protein Mokola Virus, replication origin-binding protein (UL9) of human herpes virus 1 (HHV-1), human herpes simplex helicase and Amsacta moorei […]

Pipeline specifications

Software tools UCSF Chimera, PyMOL, GROMACS