Molegro Molecular Viewer is a free cross-platform application for visualization of molecules.
http://www.molegro.com/mmv-product.php
19- Vega ZZ
Integrative drug design, docking and molecular interaction analysis
VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite.
http://users.unimi.it/~ddl/
20- Restricton enzymes double digest reaction
We have to use hundreds of restriction enzymes during our work of cloning. As every enzyme requires special conditions for proper activity it will be difficult to memorize the best conditions if we would like to combine 2 different restriciton enzymes. the tool provided in this link helps us to determine the best buffers and concentrations of resticiton enzymes if we would like to make double digest.
http://www.fermentas.com/doubledigest/index.html
21-The Basic Local Alignment Search Tool (BLAST)
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
http://blast.ncbi.nlm.nih.gov/Blast.cgi
To blast human genome
http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606
22- Protein ranking comparer
A protein fold shows different behavior in different context, for example, it can have different occurrences in different genomes, also show different transcriptome enrichment in different experiments. However, current database normally only provides the information on a protein fold itself, not on its properties in various context. Partslist can help you compare protein folds in rich context and in a unified way.
http://bioinfo.mbb.yale.edu/align/comparer/index_inter.html
23- Protein Data Bank
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards.
The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
http://www.pdb.org/pdb/home/home.do
24- Swiss-Model An Automated Comparative Protein Modelling Server
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 biochemists and molecular biologists World Wide.
a link to the first approach mode
http://swissmodel.expasy.org/workspace/index.php?func=modelling_simple1
25- pDraw
pDRAW32 lets you "clone" fragments of DNA generated by virtual digestion with restriction enzymes and optionally blunted at one or both ends. Up to 3 fragments may be cloned at a time (can you replicate that in the lab?). Each fragment may be inverted relative to its original orientation. Genetic elements contained in the cloned fragments are transferred to the cloned DNA.
pDRAW32 lets you select which restriction enzymes to plot in the graphical output and list in the textual output. To be selected an enzyme must fit all of the criteria's "Min/Max", "Seq type", and "Subset" OR the criteria "Explicit select". You may also chose to only select the explicitly selected enzymes.
Enzymes may be selected on the basis of how many times they cut in up to 5 different regions of the DNA (of which one is the entire sequence). If an enzyme cuts more than a given "Display cut off" limit, the hits and fragments are not listed in the textual output.
http://cellbiol.com/acaclone/download/install.htm
26- Genedoc
Score assisted manual alignment. Data Analysis and Visualization. GeneDoc provides tools for visualizing, editing, and analyzing multiple sequence alignments of protein and nucleic acid sequences. GeneDoc embeds these tools in an explicitly evolutionary context. This context is most directly expressed as the ability to divide the sequences into groups that reflect the division of superfamilies of genes (and proteins) into distinct families. GeneDoc can analyze and visualize these groups either separately or together.
When Similarity Groups are enabled, GeneDoc assigns amino acids to substitution groups, groups of amino acids that are treated as if they are equivalent to each other, for the purpose of measuring the degree conservation in each column of the alignment.
http://www.nrbsc.org/gfx/genedoc/index.html