Questions tagged [molecular-modeling]

Questions to do with molecular modeling.

6 questions with no upvoted or accepted answers
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How can one computationally determine the flammability of a molecular system?

I can imagine one aspect of flammability (the ability of a substance to ignite on fire) to include calculating the kinetics and thermodynamics of the reaction of the system with oxygen. This is not ...
8
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References for the Molecular Distance Geometry Problem

The molecular distance geometry problem (MDGP) consists of two sub-problems: Given observations of noisy distances between atoms in a molecule, estimate the values of the true distances. Given these ...
7
votes
0answers
48 views

Molecular Structure Vectorization for Computational Quantum Mechanics

What are the different ways that a molecule can be encoded into a vector? My answer to that question would employ machine learning but maybe there are other approaches, perhaps analytical, e.g., graph ...
7
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41 views

Transformation between two different sets of molecular vibrational normal coordinate systems

Lets assume we have $N$ Atoms and we treat them within the Born-Oppenheimer Approximation. We can calculate the adiabatic electronic groundstate potential. Lets assume we observe two local minima, ...
7
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52 views

Should one normalize the “features” in binary fingerprints?

In regression models to predict chemical compounds' activities, fingerprints are often used as features. Should one normalize a fingerprint feature to be in the 0-1 range?
6
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Construction of dimeric protein models, selection and refinement

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...