Computational Analysis Biophysical Tools '02 - Computational 11/29/2018

Sequence homologies and comparisons BLAST Expasy: http://expasy.hcuge.ch/ Entrez: NIH Other cute EXPASY tools Databases PDB SWISS-PROT SWISS-GEL Entrez (NIH) or Expasy (Switzerland, preferred) Matrix alignment: diagonals = perfect matches; off diagonals = match with inserted/deleted sequence Setup: E values Filter PROSITE identify consensus sequences pI, M wt. peptide sequences Databases PDB 3D structures of proteins and nucleic acids SWISS-PROT 70,000 sequences SWISS-GEL want a perfect gel without lifting a finger ? Biophysical Tools '02 - Computational 11/29/2018

Graphical representation cheat sheet of RASMOL commands command action select 1-9 selects residues 1 through 9 of all chains select *B selects all residues of chain B select all obvious select cys selects residues of a given type select 1-9 and *A selects residues 1 through 9 of chain A only color blue colors selected residues color [128,128,128] color defined by RGB numbers e.g. [0,0,0] black; [256,256,256] white set background white a lot of ink wasted on default black background write script filename.ras all commands in current session written to a file script filename.ras execute previously stored session spacefill 500 makes balls out of selected atoms RASMOL Grasp WebView Swiss-Prot Berkley extension Toolbox: distances, torsional angles In addition to menus of the main window: Ras Win Command Line Recall previous commands by  key Biophysical Tools '02 - Computational 11/29/2018

Secondary Structure Prediction Chou and Fasman Method Garnier Method Chou and Fasman Method the probability of certain tetrapeptide sequences to “nucleate” a given secondary structure. Many caveats and rules make it difficult to implement Garnier probability of a given amino acid to occur in certain secondary structures relies on the probability of residue i to occur in a given secondary structure and additionally considers interactions with residues along the sequence. from I-8 to i+8 Biophysical Tools '02 - Computational 11/29/2018

Biophysical Tools '02 - Computational Hydropathy Analysis Hydropathy is a scale combining hydrophobicity and hydrophilicity and can be used to predict which amino acids will be found in aqueous environments (-values) and which will be found in hydrophobic environments (+values). The scale was generated by measuring the free energy change of moving a residue from a nonpolar (low dielectric) solvent into water. Biophysical Tools '02 - Computational 11/29/2018

Biophysical Tools '02 - Computational Molecular Mechanics Quantum Mechanical Calculations Molecular Mechanics Force Fields Geometry Optimization by Energy Minimization Steepest descent Simulated annealing Quantum Mechanical Calculations The behavior of electrons in the process of bond forming and bond breaking and the exchange of electrons among energy levels is described by quantum mechanics. Ab initio calculations are based on first principles; applied only to small diatomic and organic molecules. Semiempirical calculations make a variety of approximations to reduce the amount of computer time; calculation of atomic charges and molecular orbital energy levels. Molecular Mechanics Force Fields Empirical energy functions describing the mechanical behavior of bond lengths, bond angles, dihedral angles, van der Waals and electrostatic interactions. Geometry Optimization by Energy Minimization Minimum energy structures provide better predictions of molecular properties Prepare a molecule for molecular dynamics simulations. The steepest descent method moves down the steepest slope of the potential energy function and is especially useful for eliminating close van der Waals contacts. The conjugate gradient method uses the current slope of the potential energy function and the previous search directions to drive minimization. A scaling factor is also used to optimize step sizes. Neither method and in fact no current optimization method guarantees finding the global minimum. Biophysical Tools '02 - Computational 11/29/2018

Molecular Dynamics Simulation The motion of atoms is described by Newton’s second law of motion F = ma but: F= dE/dx Where energy is given by the forcefields and atom position. Assign initial velocities according to kinetic energy ~ kT With the initial velocity and acceleration one can calculate position of any atom at the time t MD is the simulation of the motions of a atoms in a force field. The collection of forces should cause the system of atoms to change by the collective motion of particles over time. The motion of atoms is described by Newton’s second law of motion F = ma , where F is the force acting on each particle, m is the mass of a particle and a is its acceleration. Force is calculated as the negative of the first derivative of the energy function with respect to position. where F= dE/dx Newton’s equation of motion are solved by discrete numerical integration (e.g., Verlet Method) over a very large number of time steps. Assign initial velocities according to kinetic energy ~ kT To capture the highest frequency motions of bond stretching, the timestep must be on the order of 0.5 to 1.0 fs. Structural transitions It is still difficult to simulate most large scale structural changes, which usually occur on the ns time scale. Picture of a trajectory form one of Wriggers papers. Biophysical Tools '02 - Computational 11/29/2018