Welcome to PAAS Database

USAGE:

1. Search You can input keywords to search the PAAS database. Five main search categories are provided: (i) by gene/protein names, (ii) by Swiss-Prot ID/AC, (iii) by PMID or GenBank identifiers, (iv) by variants phenotype or trait ontology and (v) by amino acid substitution combinations.

2. Statistics PAAS data and statistics are presented to describe the variants collection and protein records, including the counts of organisms, PAASs, prediction of functional effects and residue environment, classification of biological phenotype as well as experimental method. These data will be recalculated as PAAS is updated.

3. Contact Users are welcome to contact us by email for any general inquiries. Also, you can revise the existed records or submit new/original proteins with novel amino acid substitutions. We are very grateful for your advice !

FAQs:

1. What do the identifiers of PAAS00001 and PAAS00001[25] mean ?

    Answer : PAAS00001 denotes an accession of protein, while PAAS00001[25] is an identifier of variants in corresponding protein. The first 4 letters of PAAS00001 are the abbreviation of Plant Amino Acid Substitution, and the last 5 digit number of PAAS00001 identifies the protein with counting in a single increment. In PAAS00001[12], the string letters and numbers before square brackets presents its protein accession, and the numbers in square brackets represents the mutational position in corresponding protein. When one original residue corresponds to multiple mutational residues, decimal point after the position numbers is added, e.g. PAAS00001[265.1] and PAAS00001[265.2].

2. What platforms does the Jmol application run on ?

    Answer : Jmol is a java applet that works in web browsers. In order to run and use it needs your system to have a suitable Java Runtime Environment (JRE) installed. Before you try to run Jmol you should therefore ensure that you have a suitable JRE. You could get JREs for different platforms available from "www.java.com". And you are strongly advised to install 64-bit Java if your system is 64-bit.

3 Where are the protein structure visualized in Jmol from ?

    Answer : The PDB structures for my analysis are obtained from PDB database if the protein structures have been solved by the experimental methods. Otherwise the PDB structures are built through homology modeling via the fully automated server, SWISS-MODEL.