Thermodynamics and kinetics of drug-target binding by molecular simulation
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
mainly thanks to improvements in hardware and algorithms. In drug discovery and …
Direct methods for computing single‐molecule entropies from molecular simulations
D Suárez, N Díaz - Wiley Interdisciplinary Reviews …, 2015 - Wiley Online Library
Assessing the actual role of entropic forces in controlling both the stability and activity of
flexible molecules and macromolecules is a theoretical challenge that is gradually gaining …
flexible molecules and macromolecules is a theoretical challenge that is gradually gaining …
Modeling intrinsically disordered proteins with bayesian statistics
The characterization of intrinsically disordered proteins is challenging because accurate
models of these systems require a description of both their thermally accessible conformers …
models of these systems require a description of both their thermally accessible conformers …
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
Motivation Protein quality assessment (QA) is a crucial element of protein structure
prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at …
prediction, a fundamental and yet open problem in structural bioinformatics. QA aims at …
Atomistic simulations of 2D bicomponent self-assembly: from molecular recognition to self-healing
Supramolecular two-dimensional engineering epitomizes the design of complex molecular
architectures through recognition events in multicomponent self-assembly. Despite being …
architectures through recognition events in multicomponent self-assembly. Despite being …
Predicting molecular self-assembly at surfaces: a statistical thermodynamics and modeling approach
Molecular self-assembly at surfaces and interfaces is a prominent example of self-
organization of matter with outstanding technological applications. The ability to predict the …
organization of matter with outstanding technological applications. The ability to predict the …
DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility
Transcription factors regulate gene expression by binding to DNA. They have disordered
regions and specific DNA-binding domains. Binding to DNA causes structural changes …
regions and specific DNA-binding domains. Binding to DNA causes structural changes …
Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints
PC Chen, S Kuyucak - Biophysical Journal, 2011 - cell.com
Free energy calculations for protein-ligand dissociation have been tested and validated for
small ligands (50 atoms or less), but there has been a paucity of studies for larger, peptide …
small ligands (50 atoms or less), but there has been a paucity of studies for larger, peptide …
Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities
The conformation adopted by a ligand on binding to a receptor may differ from its lowest-
energy conformation in solution. In addition, the bound ligand is more conformationally …
energy conformation in solution. In addition, the bound ligand is more conformationally …
Allosterism and signal transfer in DNA
We analysed the basic mechanisms of signal transmission in DNA and the origins of the
allostery exhibited by systems such as the ternary complex BAMHI–DNA–GRDBD. We found …
allostery exhibited by systems such as the ternary complex BAMHI–DNA–GRDBD. We found …