COMPUTATIONAL BIOLOGY

B.Tech – BioTech (VIth Semester)

Physical Properties Prediction

• Many of these tools are available through the ExPASy server at the Swiss Institute of Bioinformatics.

• The focus of the ExPASy tools is twofold:

– to assist in the analysis and identification of unknown proteins isolated through two-dimensional gel electrophoresis

– to predict basic physical properties of a known protein

a) AACompIdent (ExPASy)

Uses amino acid composition of an unknown protein to identify known proteins of the same composition

Input:

- desired amino acid composition

- isoelectric point (pI)

- molecular weight of the protein

- appropriate taxonomic class

- any special keywords

b) AACompSim (ExPASy)Variant of AACompIdent, performs a similar type of analysis, but rather than

using an experimentally derived amino acid composition as the basis for searches, the sequence of a SWISS-PROT protein is used instead

c) MOWSEThe Molecular Weight Search (MOWSE) algorithm based on information

obtained through mass spectrometric (MS) techniques

d) Compute pI/MW and ProtParam (ExPASy)Compute pI/MW is a tool that calculates the isoelectric point and molecular

weight of an input sequence.

e) ProtParam : calculates molecular weight, isoelectric point, overall amino acid composition, a theoretical extinction coefficient aliphatic index, the protein’s grand average of hydrophobicity (GRAVY) value

other basic physicochemical parameters.

f) TGREASETGREASE calculates the hydrophobicity of a protein along its length.

A guide to homology modeling

DOCKING?

• Docking attempts to find the “best” matching between two molecules

• The molecular docking problem:

– Given two molecules with 3D conformations in atomic detail

– Do the molecules bind to each other? If yes:

– How strong is the binding affinity?

– How does the molecule-molecule complex look like?

Goal: To be able to search a database of molecular structures and

retrieve all molecules that can interact with the query

structure

Why is docking important?

• It is of extreme relevance in cellular biology, where function is accomplished by proteins interacting with themselves and with other molecular components

• It is the key to rational drug design: The results of docking can be used to find inhibitors for specific target proteins and thus to design new drugs. It is gaining importance as the number of proteins whose structure is known increases

Docking problems can be best classified by the type of input molecules:

• Macromolecule Docking- Protein-Protein docking- Protein-DNA docking

• Small molecule docking• Protein-Ligand docking

- rigid-body docking- flexible docking

• DNA-Ligand docking

1. Macromolecular docking• two macromolecules are docked, such as protein and DNA, or

protein and protein• large contact area• molecules have fixed overall shape• methods based on geometric properties like shape

complementarities alone can be efficiently used to create energetically favorable complexes

2. Small molecule docking• a small molecule is docked to a macromolecule• ligand is typically not fixed in shape (as opposed to

macromolecular docking)• typical ligand size has 5-12 rotatable bonds• often fragments of ligand are used for modeling, eg.

combinatorial libraries are docked by combining placement for individual building blocks of the library

• Rigid-body docking algorithms– Historically the first approaches. – Protein and ligand are held fixed in conformational space

which reduces the problem to the search for the relative orientation of the two molecules with lowest energy.

– All rigid-body docking methods have in common that superposition of point sets is a fundamental sub-problem that has to be solved efficiently:

– Superposition of point sets: minimize the RMSD

• Flexible ligand docking algorithms– most ligands have large conformational spaces with several

low energy states

MOLECULAR DOCKING

• Docking is the process of predicting the protein-ligand complexes in which the ligand molecules interact with the binding site of receptor. The ligand protein interactions are of various types i.e. vanderwaals, electrostatic , hydrogen bonding etc

Electrostatic energy can be expressed as the inverse of the distance of the interacting atoms, Whereas the steric energy depends on its inverse twelfth power. Thus at long distances the electrostatic field drives the approach of the ligand to the active site, whereas at short ranges the steric forces (van der waal) become important and control the final step of binding.

Active Site Prediction• The region of the enzyme containing the binding and catalytic

sites is called the active site.

• Usually occurs near or on the surface of the protein as a cleft for the substrate to fit.

• Active site depends on a variety of factors from the sequence of amino acids (primary structure) to arrangement of protein chain in space and time (secondary, tertiary and quaternary structures).

• Different approaches for active site identification are:– Geometrical approach

– Physicochemical approach

– Machine –learning approach

Rigid Body Docking: Clique-search based approaches

• match characteristic features of the two molecules • use a graph to search for compatible matches: the vertices of

the graph are all possible matches and edges connect pairs of vertices representing compatible matches

• compatibility = distance compatibility with in a fixed tolerance epsilon

• The matches (p1,l1), (p2,l2) are distance-compatible if |d(p1,p2)-d(l1,l2)| < epsilon

• Example: DOCK program

DOCKToday most widely used molecular docking program

• starting with the molecular surface of the protein , a set of spheres is created inside the active sties

• the spheres represent the volume which could be occupied by the ligand: VOLUME is the feature used for matching

• ligand is represented by spheres inside the ligand

For more information: http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm

(Assisted Model Building with Energy Refinement)

Mechanism of drug binding:

Ligand binding mechanism

If one fails to find a molecule with the required interacting groups

by database searching methods or docking , then the alternative is

to construct a ligand having the active groups placed in a way that

can interact with the interaction sites identified earlier. This ligand

construction process is called de novo ligand design.

Three categories of de novo ligand design are

• Linking

• Growing

• Random connection

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