Evaluation of the Molecular Configuration Integral in All Degrees of Freedom for the Direct Calculation of Binding Free Energies:  Application to the Enantioselective Binding of Amino Acid Derivatives to Synthetic Host Molecules

1997 ◽  
Vol 119 (42) ◽  
pp. 10233-10234 ◽  
Author(s):  
István Kolossváry
Keyword(s):  
Amino Acid ◽  
Degrees Of Freedom ◽  
Direct Calculation ◽  
Amino Acid Derivatives ◽  
Free Energies ◽  
Molecular Configuration ◽  
Host Molecules ◽  
Configuration Integral ◽  
Binding Free Energies

Direct calculation of the binding free energies of FKBP ligands

2005 ◽  
Vol 123 (8) ◽  
pp. 084108 ◽  
Author(s):  
Hideaki Fujitani ◽  
Yoshiaki Tanida ◽  
Masakatsu Ito ◽  
Guha Jayachandran ◽  
Christopher D. Snow ◽  
...  
Keyword(s):  
Direct Calculation ◽  
Free Energies ◽  
Binding Free Energies

scholarly journals The role of water in host-guest interaction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Valerio Rizzi ◽  
Luigi Bonati ◽  
Narjes Ansari ◽  
Michele Parrinello
Keyword(s):  
Ligand Binding ◽  
Degrees Of Freedom ◽  
Enhanced Sampling ◽  
Free Energies ◽  
Collective Variables ◽  
Complex Behaviour ◽  
Field Quality ◽  
Non Local ◽  
Binding Free Energies

AbstractOne of the main applications of atomistic computer simulations is the calculation of ligand binding free energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling is an obstacle in simulations due to the frequent appearance of kinetic bottlenecks in the free energy landscape. Very often this difficulty is circumvented by enhanced sampling techniques. Typically, these techniques depend on the introduction of appropriate collective variables that are meant to capture the system’s degrees of freedom. In ligand binding, water has long been known to play a key role, but its complex behaviour has proven difficult to fully capture. In this paper we combine machine learning with physical intuition to build a non-local and highly efficient water-describing collective variable. We use it to study a set of host-guest systems from the SAMPL5 challenge. We obtain highly accurate binding free energies and good agreement with experiments. The role of water during the binding process is then analysed in some detail.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

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