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

2. Sequence homologies and comparisons
BLAST
Expasy: 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

3. 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

4. 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

5. 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

6. 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

7. 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