title: MAP(2.0)3D: a sequence/structure based server for protein engineering.
abstract: The Mutagenesis Assistant Program (MAP) is a web-based tool to provide statistical analyses of the mutational biases of directed evolution experiments on amino acid substitution patterns. MAP analysis assists protein engineers in the benchmarking of random mutagenesis methods that generate single nucleotide mutations in a codon. Herein, we describe a completely renewed and improved version of the MAP server, the MAP(2.0)3D server, which correlates the generated amino acid substitution patterns to the structural information of the target protein. This correlation aids in the selection of a more suitable random mutagenesis method with specific biases on amino acid substitution patterns. In particular, the new server represents MAP indicators on secondary and tertiary structure and correlates them to specific structural components such as hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and crystallographic B-factors. Three model proteins (D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase) are used to illustrate the novel capability of the server. MAP(2.0)3D server is available publicly at http://map.jacobs-university.de/map3d.html.
authors: School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
authors: Rajni
authors: R
authors: Verma
authors: Ulrich
authors: U
authors: Schwaneberg
authors: Danilo
authors: D
authors: Roccatano
mesh_terms: D010832:6-Phytase / Q000737:chemistry / Q000235:genetics; D019943:Amino Acid Substitution; D003605:D-Amino-Acid Oxidase / Q000737:chemistry / Q000235:genetics; D019020:Directed Molecular Evolution; D021621:Imaging, Three-Dimensional; D020407:Internet; D008958:Models, Molecular; D016296:Mutagenesis; D007652:Oxo-Acid-Lyases / Q000737:chemistry / Q000235:genetics; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods* / Q000706:statistics & numerical data; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D012984:Software; D058615:Synthetic Biology
chemical_list: D011994:Recombinant Proteins; D003605:D-Amino-Acid Oxidase; D010832:6-Phytase; D007652:Oxo-Acid-Lyases; C018728:N-acetylneuraminate lyase