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Questions tagged [chimera-software]

Questions about or related to UCSF Chimera, the software for interactive visualization and analysis of molecular structures and related data.

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4 votes
1 answer
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Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
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3 votes
1 answer
71 views

Perform energy minimization of multiple models of protein-dna complexes

Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)? I know of GROMACS or Chimera or the online servers but is ...
Lily Sharpton's user avatar
4 votes
1 answer
527 views

Ligand-protein molecular docking with different protonation states

It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational ...
SharkCaller's user avatar