<p>(A) Correlation diagram showing the change in non-bonded interaction energies (electrostatic – top, van der Waals – bottom) for relevant binding site residues (y-axis) upon a given alanine mutation (x-axis). Only residues with any absolute interaction energy change above 1 kcal/mol are shown, where the water molecules are present throughout the MD simulations and also observed in the crystal structure. (B) The corresponding affected residues and water molecules are shown in sticks for the initial 3D structure of the complex.</p
Here, we show that alchemical free energy calculations can quantitatively compute the effect of muta...
<p>(A) PCA loading plot for training-set van der Waals interaction energies; (B) Active site of CYP ...
<p><b>A.</b> The predicted structure of the wild-type MKK4-JNK3 complex with predicted binding energ...
<p>(A) Starting structure used for the FEP simulations with TM helices shown and colored according t...
<p>(A) Starting structure used for the FEP simulations, with explicit representation of residues sub...
<div><p>To predict structural and energetic effects of point mutations on ligand binding is of consi...
To predict structural and energetic effects of point mutations on ligand binding is of considerable ...
<p>Free energy changes for hydrophobic residues, charged residues, and only charged residues that ar...
To predict structural and energetic effects of point mutations on ligand binding is of considerable ...
<p>Both ligand and binding site plasticity contributes to changes in the binding mode between the li...
Most physiological processes in living systems are fundamentally regulated by protein–ligand interac...
Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as...
Here, we show that alchemical free energy calculations can quantitatively compute the effect of muta...
<p>Residues identified as warm/hot-spots by <i>pr</i>EFED were selected for CAS, except for Cys, Pro...
Most physiological processes in living systems are fundamentally regulated by protein–ligand interac...
Here, we show that alchemical free energy calculations can quantitatively compute the effect of muta...
<p>(A) PCA loading plot for training-set van der Waals interaction energies; (B) Active site of CYP ...
<p><b>A.</b> The predicted structure of the wild-type MKK4-JNK3 complex with predicted binding energ...
<p>(A) Starting structure used for the FEP simulations with TM helices shown and colored according t...
<p>(A) Starting structure used for the FEP simulations, with explicit representation of residues sub...
<div><p>To predict structural and energetic effects of point mutations on ligand binding is of consi...
To predict structural and energetic effects of point mutations on ligand binding is of considerable ...
<p>Free energy changes for hydrophobic residues, charged residues, and only charged residues that ar...
To predict structural and energetic effects of point mutations on ligand binding is of considerable ...
<p>Both ligand and binding site plasticity contributes to changes in the binding mode between the li...
Most physiological processes in living systems are fundamentally regulated by protein–ligand interac...
Using the MP1-p14 scaffolding complex from the mitogen-activated protein kinase signaling pathway as...
Here, we show that alchemical free energy calculations can quantitatively compute the effect of muta...
<p>Residues identified as warm/hot-spots by <i>pr</i>EFED were selected for CAS, except for Cys, Pro...
Most physiological processes in living systems are fundamentally regulated by protein–ligand interac...
Here, we show that alchemical free energy calculations can quantitatively compute the effect of muta...
<p>(A) PCA loading plot for training-set van der Waals interaction energies; (B) Active site of CYP ...
<p><b>A.</b> The predicted structure of the wild-type MKK4-JNK3 complex with predicted binding energ...