Welcome to MAP2.03D Server
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Welcome to the Mutagenesis Assistant Program
 

Mutagenesis Assistant Program server analyses the consequences of mutational bias on amino acid substitution patterns in proteins. The server performs statistical analysis on nucleotide sequence for 19 commonly used random mutagenesis methods.

MAP2.03D server is the new improved version of our currently running MAP server. It extends the sequence based MAP analysis by correlating it with global and local structural properties of the target protein, which generally influences the acceptance of amino acid substitution. The structural properties taking into account are local structural component (e.g. hydrogen bonds, hydrophobic contacts), which contribute defining protein secondary structure, residue flexibility and solvent accessibility.

The new server provides the results of the analysis in both tabular and graphical format and mapping the information on the 3D structure of the target protein. Target based query system is implemented in this version which facilitates to fetch the statistical analysis of amino acid substitution probability with structural information of the specified region in the protein. It helps to explore the random mutagenesis methods in a structure guided and property specific manner by focusing on the effect of mutational spectra on a set of amino acid residues responsible for the stability and activity of the protein. In addition, the new server allows to extend the analysis to user defined mutagenesis methods and to change the default parameters to customize the structural analysis. The MAP2.03D server is a very useful tool for the protein engineers to help designing directed enzyme evolution campaigns by the in silico benchmarking of different random mutagenesis method.

 
Citations
For publication of the results, please cite:
MAP2.03D: A sequence/structure based server for protein engineering
Verma R, Schwaneberg U & Roccatano D 2012. ACS Synth Biol, DOI: 10.1021/sb200019x [doi]
A statistical analzsis of random mutagenesis methods used for directed evolution
Wong TS, Roccatano D, Zacharias M & Schwaneberg U 2006. J Mol Biol, 355, 858-871 [doi]
 
Table summarizing the difference between MAP and MAP2.03D
 
FEATURE MAP MAP2.03D
Input data Nucleotide Sequence Nucleotide sequence, PDB structure, method
Protein structure indicator Yes Yes
Amino acid diversity indicator Yes Yes
Chemical diversity indicator Yes Yes
Amino acid substituion pattern No Yes
Amino acid substituion mapping on structure No Yes
Amino acid substitution with molecular interactions No Yes
Target based query system No Yes
User defined mutagenesis method No Yes
 
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Disclaimer: This server and its associated data and services are for research purpose only, not for clinical or commercial use. It is a non-profit service to the scientific community. The responsibility of the authors is limited to applying best efforts in providing and publishing good programs and data. The authors have no responsibility for the use of results, data or information which have been provided through this server.

Reference: Verma R, Schwaneberg U, Roccatano D 2012. MAP2.03D: A sequence/structure based server for protein engineering  
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