Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes....
Ligand docking referred to cases where small molecule (“ligand”) is being docked into much larger macromolecule ("target"). The following is partial list of docking software, focusing on free (at least for academic institutes) and/or...
The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues...
The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the...
Awk is a programming language which allows easy manipulation of structured data and is mostly used for pattern scanning and processing. It searches one or more files to see if they contain lines that match with the specified patterns and then...
BBSplit internally uses BBMap to map reads to multiple genomes at once, and determine which genome they match best. This is different than with ordinary mapping. If a genome (say, human) contains an exact repeat somewhere, reads mapping to it will...
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something.
As with most programs that run on UNIX, the text output is in some specific...
analog -- A feature that appears similar in two taxa which have originated from two different ancestors.
ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by...
