A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Jan 15, 2011

Structural Biology


ModWeb:

Modweb is a Server for Protein Structure Modeling.
Website:     https://modbase.compbio.ucsf.edu/scgi//modweb.cgi

What if web server:

The program WHAT IF provides nearly 2000 options in fields as diverse as homology modelling, drug docking, electrostatics calculations, structure validation and visualisation for researchers The what if web server gives everybody access to some of the options available in the what if program.

Website : http://swift.cmbi.ru.nl/servers/html/index.html

Swiss-Model

SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all researchers WorldWide.

Website : http://swissmodel.expasy.org/

ESyPred3D 

ESyPred3D is a new automated homology modeling program. The method gets benefit of the increased alignment performances of a new alignment strategy using neural networks. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three dimensional structure is built using the modeling package MODELLER.

Website : http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/

PSIPRED

The PSIPRED Protein Structure Prediction server can Predict Secondary Structure, Predict Transmembrane Topology , Fold Recognition given a sequence.

Website : http://bioinf.cs.ucl.ac.uk/psipred/

PDB2PQR :

This server enables a user to convert PDB files into PQR files. PQR files are PDB files where the occupancy and B-factor columns have been replaced by per-atom charge and radius.

Website :  http://kryptonite.nbcr.net/pdb2pqr/

H++ server

H++ is an automated server that computes pK values of ionizable groups in macromolecules and adds missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the completed structure in several common formats (PDB, PQR, AMBER inpcrd/prmtop) and provides a set of tools useful for analysis of electrostatic-related molecular properties.

Website : http://biophysics.cs.vt.edu/H++/

PDB to MultiGIF

Visualization of chemical 3D structures on the web comes with problems because the web browser cannot display chemical structures without the help of additional software. If you create a page with a 3D structure of a molecule and the visitor of your page does not use this special viewer software for displaying molecules it cannot get the whole information of the page which should be meditated.

PDB2MultiGIF takes the 3D structure and generates an animated image which can be displayed using any browser. Thus every visitor of your page can get the whole information.isualization of chemical 3D structures on the web comes with problems because the web browser cannot display chemical structures without the help of additional software. If you create a page with a 3D structure of a molecule and the visitor of your page does not use this special viewer software for displaying molecules it cannot get the whole information of the page which should be meditated.

PDB2MultiGIF takes the 3D structure and generates an animated image which can be displayed using any browser. Thus every visitor of your page can get the whole information.

Website : http://www.glycosciences.de/modeling/pdb2mgif/

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