| 3D | three-dimensional (co-ordinates of protein structure) |
| 2D | 2D two-dimensional (e.g. inter-residue contacts) |
| 1D | 1D one-dimensional (e.g. sequence or string of secondary structure) |
| db | database |
| ORF | open reading frame |
| U | protein sequence of unknown 3D structure and/or unknown function (e.g. search sequence in alignment procedure) |
| T | target used for homology modelling (protein of known 3D structure) |
| sequence identity | percentage of residues identical (D->E = 0; D->D = 1) between two sequences aligned (insertions excluded) |
| sequence similarity | percentage of residues similar (D->E = 1; D->D = 1) between two sequences aligned (insertions excluded); there are two ways to convert similarity into percentage values: (i) by normalising the similarity score by the maximal possible score (percentage residue similarity), and (ii) by setting an arbitrary threshold of the similarity score to distinguish similar-not similar and counting the percentage of residues that are similar according to this threshold (percentage of similar residues); note that different similarity metrices are used to account for physico-chemical properties of amino acids, consequently, levels of similarity are usually not directly comparable between different alignment methods) miscellaneous |
| browser | program used to access the WWW |
| CPU | Central Processing Unit, i.e., 'core' of the computer |
| ftp | file transfer protocol, i.e., program to copy files via the internet |
| HTML | HyperText Markup Language, i.e., format of a WWW document |
| Internet | most important network connecting computers worldwide |
| plug-in | module to be plugged into your WWW browser, provides special functionality, such as graphics to display 3D structures |
| URL | Uniform Resource Locator, i.e., address of a WWW site (in other words the address you have to provide to open a location) |
| WWW | (W3, Web) World Wide Web, i.e., vehicle for accessing and offering documents via the Internet |
