Computational systems biology-Tool

If Molecular Biology is Tree -System Biology is Forest .System biology is not pathways but networks…stupid. A Pathways is a specific path through the network.The information we are finding represents the “parts” of the system, when we move into the realm of establishing functionality of the system we are determining the blueprints for these part.
Tools & Software in Computational Systems Biology:
1)Cell Designer
2)CellWare 

3)Dynetica

4)E-Cell 

5)Gepasi

6)SmartCell 

7)Vcell

8)Snoopy

9)CPN Tools

10)BioSPI  

11)CancerSim

12)Mcell 

13)SimCell

14)AgentCell 

15)Cell Illustrator- Animator

Docking With HEX

1. Remove water and other Hetero atoms from receptor using heterocontrol panal or manually. . Remove peptidechain which might not necessary for docking.

2. Open receptor and ligand using file ? open ? receptor and ligand options.

3. Go to Graphics ? Hormonic surface

4. Select apply to Receptor and change display mode polygons and click enable surface.

5. Select apply to ligand and change display mode polywire and click hex mesh.

6. Go to Controls ? orientation control.

7. Select move to ligand and click fit ligand option and then click commit button.

8. Go to controls ? Docking control

9. Select correlation type shape + electrostatic

10. Select post processing type energyminimization

11. Then activate docking.

12. After completion of docking file ? save ? both option to save docked image

13. File ? save ? docking option might be used to save energy details.

14. Message might be saved to see the progress of docking.

Docking software

ArgusLab:Drug design program

Materials Studio: software environment

MOE:Molecular Operating Environment

Hex:Protein-Protein Docking

PCMODEL:common molecular modeling tool

Molecular Docking

In the field of molecular modeling,docking is a method which predicts the preferred orientation of one molecule to a second when boundto each other to form a stablecomplex.Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinitybetween two molecules using for examplescoring functions.

Receptor or host – The "receiving" molecule, most commonly a protein or otherbiopolymer.

Ligand or guest – The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer.

Docking – Computational simulation of a candidate ligand binding to a receptor.

Binding mode – The orientation of the ligand relative to the receptor as well as theconformation of the ligand and receptor when bound to each other.

Pose – A candidate binding mode.

Scoring – The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts.

Ranking – The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding.

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more info

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http://www.nia.nih.gov/Alzheimers/

Viewing Three Dimensional Structures

 

BioEditor (Peng Yang, Paul A. Craig, Philip E. Bourne, & David Goodsell, San Diego Supercomputer Center, U.S.A.) - is a tool to bridge the gap between the printed literature and current Internet presentation formats.

This application that can be used to prepare and present structure annotations containing formatted text, graphics, sequence data, and interactive molecular views. It require that MDL Chime be installed. 

Yasara (Gregor Högenauer, Günther Koraimann, & Andreas Kungl [Univ. Graz, Austria]; & Gert Vriend [Univ. Nijmegen, the Netherlands]) is an awesome program for viewing an labeling 3-D structures. To visual your own pdb structure right click and chose open with (Yasara). This free program is part of a more extensive molecular modeling package.

NOC (Chenmengen & Cang, Institute of Biophysics, Chinese Academy of Sciences [IBP-CAS]) is a program to model/build, visualize and analysis protein structure and includes: easy addition/delete of water and heteroatoms, comparison of similar structures, predict possible motifs (sites) in the molecule, high quality rendering and many types of output (such as TIFF, PNG, BMP), and WYSIWYG labeling method.

ArgusLab (Mark A. Thompson, Planaria Software LLC, Seattle, U.S.A.) is an incredible molecular modeling, graphics, and drug design program.

RasMol is software for looking at molecular structures. It is very fast: rotating a protein or DNA molecule shows its 3D structure. 

Deep View (Swiss-PdbViewer) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface Scion Image may be used to capture, display, analyze, enhance, measure, annotate, and output images.

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR.

Biodesigner is a molecular modeling and visualization program for personal computers which is capable of creating homologous models of proteins, evaluate, and refine the models. 

RasTop - RasTop is a molecular visualization software adapted from the program RasMol by wrapping a user-friendly graphical interface around the "RasMol molecular engine". The software allows several molecules to be opened in the same window and several windows to be opened at the same time. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

Protein Analysis

ANTHEPROT:- (Analyse The Proteins) is the result of biocomputing activity at the Institute of Biology and Chemistry of Proteins (Lyon, France)

STORM: - this program extracts protein sequences after ORF prediction and subsequently performs an automatic analysis for each of the proteins. This analysis consists of web-based similarity searches (BLASTp and FASTA) as well as Pfam predictions and Protparam calculations of protein physicochemical properties. The raw output for these analyses is then analysed and summarized. (Reference: Lavigne, R. et al. (2003.) Applied Bioinformatics 2: 177-179).

WinPep: - WinPep ( is a versatile tool for the analysis of protein sequences (determination of amino acid composition, molecular weight, isoelectric point, & potential posttranslational modifications. It also will search for sequence motifs, display of amino acid sequences as helical wheels, hydropathy plots, & domain structure of proteins). (Reference: L. Hennig (1999) BioTechniques 26: 1170-1172 )