Protein & DNA: Molecular Dynamics Analysis
Budget: $30 – $250 USD
I'm conducting a comprehensive study on protein and DNA interaction through molecular dynamics.
Key requirements:
- Expertise in data analysis focusing on molecular interactions
- Proficiency in molecular dynamics simulations
Molecular analysis of a protein and dna
Given a protein, DNA sequence, and specific binding site. Evaluate how to corroborate or not the hypothesis that the protein interacts with the DNA, the total binding energy has been calculated already, as well as the LAMMPS simulation for such system. However, it has been requested that a quantitative method is developed to prove or disprove such hypothesis, and to describe the interaction between the protein and DNA.
Please provide a script, results, and graphed results for the mechanisms you propose could be used to prove such hypothesis.
Suggested options:
Which type of bond is happening between the protein and DNA. Can you say how many bonds?
Are the protein and DNA getting closer, how is the distance changing with time?
If the water and ions are interacting with the structure, how? and prove it quantitatively.
Key requirements:
- Expertise in data analysis focusing on molecular interactions
- Proficiency in molecular dynamics simulations
Molecular analysis of a protein and dna
Given a protein, DNA sequence, and specific binding site. Evaluate how to corroborate or not the hypothesis that the protein interacts with the DNA, the total binding energy has been calculated already, as well as the LAMMPS simulation for such system. However, it has been requested that a quantitative method is developed to prove or disprove such hypothesis, and to describe the interaction between the protein and DNA.
Please provide a script, results, and graphed results for the mechanisms you propose could be used to prove such hypothesis.
Suggested options:
Which type of bond is happening between the protein and DNA. Can you say how many bonds?
Are the protein and DNA getting closer, how is the distance changing with time?
If the water and ions are interacting with the structure, how? and prove it quantitatively.