Scribd
Upload
1K views6 pages

Molinspiration Chembioinformatics

This document discusses various software tools used in drug design and development including: 1. Molinspiration and Osiris Property Explorer which evaluate chemical properties and bioavailability of ligands. 2. Docking software like AutoDock which checks the interaction of ligand molecules with target proteins. 3. Modeling software like Modeller which predicts protein structures based on homology modeling. 4. Other software mentioned include LigSite for active site prediction, ChemSketch for structure drawing and optimization, HEX for docking, and LigBuilder for growing ligands.

Uploaded by

bedibedi
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOC, PDF, TXT or read online on Scribd
1K views6 pages

Molinspiration Chembioinformatics

This document discusses various software tools used in drug design and development including: 1. Molinspiration and Osiris Property Explorer which evaluate chemical properties and bioavailability of ligands. 2. Docking software like AutoDock which checks the interaction of ligand molecules with target proteins. 3. Modeling software like Modeller which predicts protein structures based on homology modeling. 4. Other software mentioned include LigSite for active site prediction, ChemSketch for structure drawing and optimization, HEX for docking, and LigBuilder for growing ligands.

Uploaded by

bedibedi
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as DOC, PDF, TXT or read online on Scribd
You are on page 1/ 6

Molinspiration chembioinformatics : It evaluates the chemical properties and

bioavailability of the ligand molecules.

Osiris pro[perty expolorer :


It evaluates the chemical and other properties like mutagenesis, toxicity etc.

Docking :
It is the process to check the interaction of ligand molecule with the protein .here the
second type of docking is performed-flexible docking .
Flexible docking is the process to check the bindind energy of various rotamers of ligand
molecule and protein complex. The complex with least binding energy as compared to
the protein –substrate is calculated .the resulting legand with least energy in docking may
act a possible drug molecule .

Input file:protein file(.pdb).


The ligand selected in ADME/TOX evaluated (.pdb)

Output file : the resultant file(.dlg)

Software used:
1.visuaisation swiss-pdv
2.modeling modeller
3.Active site prediction ligsite
4.3-D structure optimization chemsketch
4.Ligand screening hex 4.5
5.Ligand generation and optimization ligbuilder
6.Drug validation osiris property explorer
7.Docking autodock

Swiss-pdb viewer:a visualization tool used to view actual 3-dimensional structure of


protein .

Uses of pdb;
1.to view the protein nstructure .
2.to view the active site in proteins.
3.to finf=d the closet residue from ASP.
4.for the rifenement of protein structure.
5.to view the ramachandran plot for protein.

Modeler :modeler 9v3 is used to find out the structure of target protein in case the
structure is not available I n pdb.modeller ha sits own library of all amino acids .
Principle :it is based on the principle of satisfaction of spatilka restraints.

Input files:alignment file(.ali)


Atomic co-ordinates file(.atm)
Python file(.py)

Output file: possible target protein structures(.pdb)

Ligsite : use dto identify the pockets\active sites of the regard protein.
It is available under the server of Dresden university ,denmark can be accsed through
google.

Input file : protein structure file(.pdb)

Output file : protein_pocket file(.pdb)

Chemsketch: chemsketch10.0,it is simply a computional chemistry software ,it has an


interface of 3-dimensional viewer with 3-d optimizer tool and a drawing pad.

Drawing a lead  virtual structure of lead (.mol)

Hex: introduction of lead into active is done through software hex 4.5 .hex is an
interactive protein docking and molecular superposition program, written by dave Ritchie
.hevx performs the rigid doclking using lmolecular docking and fourier transformations,
by changing the orientation of the lead molecule it checks the interaction of protein and
lead molecule and thus introduce the lead into cavity.

Input file for hex : protein (.pdb)


Lead molecule (.pdb)

Output file : protein- lead complex file (.pdb)


Ligbuilder : it is used for growing the lead into ligand molecule . ligbuilder 1.2 is a
software basically developed for open source environment software . but can also work in
encrypte denvirnment with c compiler .

Ligbuilder has three functionalities with two strategies :

1.pocketing
2.growing ang linling {strategies}
3.processing.

Osiris property explorer: the osiris property explorer shwn in this page is an integral
part of actelation’s(1) inhouse substance registration system.it lets you draw chemical
structures and calculates on-the fly various drug-relevant properties whenever a structure
is valid .
It is used to analyze the properties like –toxicity,mutagenic nature ,irritant nature
,reproductive effect ,drug score etc.

Autodoc : a most preferred software for docking ,that perform the flexi ble docking .
flexible docking os the process to check the binding energy of various rotamers of ligand
molecule and protein complex. The complex with least binding energy as compared to
ythe protein –substrate is calculated .the resulting ligand with least energy in docking
may act a possible drug molecule .

Input file : protein file (.pdb)

The ligand selected in ADME/TOX evaluated (.pdb)

Output file : the resultant file (.dlg)


Theory behind …….

Homology modeling ;
With the development of techniques in molecular biology that allow rapid
identification,isolation and sequencing of genes , we are now able to infer the sequences
of many proteins .however., it is still a time-consuming task to obtain the three –has
dimensional of these proteins.a major goal of structural biology is to predict the three-
dimensional structure from the sequence , a pursuit that not yet been realized.thus,
alternative strategies from x-ray diffraction or NMR are not yet.

One method that can be applied to generate reasonable models of protein structures is
homology modeling .this procedure , also termed comparative modeling or knowledge –
Based modeling ,develops a three dimensional model from a proein sequence based on
the structures of homologous proteins . several reviews on this topic have appeared [1-5].
In the description that follows , some aspects of homology modeli ng that you find useful
in this course and in your research are disscused.

General procedure :

The steps to creating a homology model are as follows :


1.identify omolgous proteins and determine the extent of their sequence similarity with
one another and the unknown.
2.align the sequence .
3.identify structurally conserved and structurally variable regions.
4.generate coordinates for core (structurally conserved) residue of the unknown structure
from those of the unknown structure(s)
5.generatre conformations for the loops(structurally variable )in the unknown structure .
6.build the side chain conformations .
7.refine and evaluate the unknown structure .

Lipinkins rule of five analysis ;

Christoper lipinkins rule-of-five analysis helped to raise awareness about properties and
structural features that make molecule more or less drug like .the guidelines were quickly
adopted by the pharmaceutical industry as it helped apply ADME considerations early in
preclinical development and could help avoid costly late-stage preclinical and clinical
failures.the guidelines predict that poor absorption or permaeation of a orally
administrated compound are more likely if the compound meets the following criteria:

Molecular mass greater than 500 Da .


High lipophilicity(expressed as cLog P greater than 5)
More than 5 hydrogen bond donors
More than 10 hydrogen bond acceptors.

Ramachandran plot ;

A ramachandran plot (also known as a ramachandran map or a (ramachandran diagram ).


Developed by gopalasamudran narayana ramachandran ,is a way to visualize dihedral
angles φ against ψ of amino acid residue in protein structure .it shows the possible
conformations of φ and ψ angles for a lpoypeptide .

You might also like

pFad - Phonifier reborn

Pfad - The Proxy pFad of © 2024 Garber Painting. All rights reserved.

Note: This service is not intended for secure transactions such as banking, social media, email, or purchasing. Use at your own risk. We assume no liability whatsoever for broken pages.


Alternative Proxies:

Alternative Proxy

pFad Proxy

pFad v3 Proxy

pFad v4 Proxy