MINIMUTATE: MINIMIZATION ON MUTATED PROTEIN STRUCTURE

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KHOSHNEJAT MARYAM; ARAB SEYED SHAHRIAR

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Journal Paper

Paper Information

Journal: MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS Year:2014 | Volume:3 | Issue:SUPPL. (1) Page(s): 192-192

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Title

MINIMUTATE: MINIMIZATION ON MUTATED PROTEIN STRUCTURE

Author(s)

KHOSHNEJAT MARYAM | ARAB SEYED SHAHRIAR

Keywords

SITE DIRECTED MUTAGENESIS

PROTEIN ENGINEERING

MINIMIZATION

MISSING ATOMS

Abstract

There is an increasing trend towards the engineering characteristics and utility of proteins in order to the industrial, biotechnological and biopharmaceutical applications. Lots of protein manipulations can be achieved through SITE DIRECTED MUTAGENESIS. It is expensive and time consuming to analyze the effect of mutation by getting an X-ray structure of mutant proteins. The use of predictive computational methods has become more prevalent in recent years leading to decrease the cost of experiments. Therefore, it is needed and common to predict the influence of engineering on protein structure with molecular dynamics (MD) simulation before going to the experiment. In this work, the software “MiniMutate” has been developed which can do a single mutation in a protein structure. Mutant coordinate file which is generated after the local and the global MINIMIZATION with molecular dynamics program NAMD will be returned as the output. This file can be used as an input of MD simulation packages. In comparison to similar software at WHATIF server, MiniMutate can do mutation in a specific chain that user is selected, the important option which is lacking on WHAT IF, and with minimizing mutant structure it can be more precision than the WHAT IF output. In addition, this software can be used to construct missing side chains from PDB file. The software is freely available at: http://bioinf.modares.ac.ir/software/minimutate/.

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APA: Copy

KHOSHNEJAT, MARYAM, & ARAB, SEYED SHAHRIAR. (2014). MINIMUTATE: MINIMIZATION ON MUTATED PROTEIN STRUCTURE. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS, 3(SUPPL. (1)), 192-192. SID. https://sid.ir/paper/336141/en

Vancouver: Copy

KHOSHNEJAT MARYAM, ARAB SEYED SHAHRIAR. MINIMUTATE: MINIMIZATION ON MUTATED PROTEIN STRUCTURE. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS[Internet]. 2014;3(SUPPL. (1)):192-192. Available from: https://sid.ir/paper/336141/en

IEEE: Copy

MARYAM KHOSHNEJAT, and SEYED SHAHRIAR ARAB, “MINIMUTATE: MINIMIZATION ON MUTATED PROTEIN STRUCTURE,” MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS, vol. 3, no. SUPPL. (1), pp. 192–192, 2014, [Online]. Available: https://sid.ir/paper/336141/en

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