Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation
Shailesh Kumar Panday, Emil Alexov
Abstract
values. This data set has been used for benchmarking in recently published protein-protein binding studies that apply conventional MM/PBSA and MM/PBSA with an enhanced sampling method. The f5-MM/PBSA/E tested on the same data set achieves similar or better performance than these computationally demanding approaches, making it an excellent choice for high throughput protein-protein binding affinity prediction studies.
Topics & Concepts
SolvationGaussianConformational entropyImplicit solvationEntropy (arrow of time)Dissociation constantChemistryMolecular mechanicsAccessible surface areaTitinMolecular dynamicsStatistical physicsThermodynamicsComputational chemistryMoleculePhysicsSolventBiochemistrySarcomereOrganic chemistryEndocrinologyReceptorMedicineMyocyteProtein Structure and DynamicsEnzyme Structure and FunctionComputational Drug Discovery Methods