Experimental binding energies in supramolecular complexes

F Biedermann, HJ Schneider - Chemical reviews, 2016 - ACS Publications
On the basis of many literature measurements, a critical overview is given on essential
noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses …

The molecular origin of enthalpy/entropy compensation in biomolecular recognition

JM Fox, M Zhao, MJ Fink, K Kang… - Annual Review of …, 2018 - annualreviews.org
Biomolecular recognition can be stubborn; changes in the structures of associating
molecules, or the environments in which they associate, often yield compensating changes …

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

H Sun, L Duan, F Chen, H Liu, Z Wang, P Pan… - Physical Chemistry …, 2018 - pubs.rsc.org
Entropy effects play an important role in drug–target interactions, but the entropic
contribution to ligand-binding affinity is often neglected by end-point binding free energy …

The roles of water in the protein matrix: a largely untapped resource for drug discovery

F Spyrakis, MH Ahmed, AS Bayden… - Journal of medicinal …, 2017 - ACS Publications
The value of thoroughly understanding the thermodynamics specific to a drug
discovery/design study is well known. Over the past decade, the crucial roles of water …

The Role of Packing, Dispersion, Electrostatics, and Solvation in High‐Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests

LM Grimm, S Spicher, B Tkachenko… - … A European Journal, 2022 - Wiley Online Library
The rationalization of non‐covalent binding trends is both of fundamental interest and
provides new design concepts for biomimetic molecular systems. Cucurbit [n] urils (CBn) are …

Interaction of amino acids and graphene oxide: trends in thermodynamic properties

S Pandit, M De - The Journal of Physical Chemistry C, 2017 - ACS Publications
Recent studies on interaction of graphene oxide with proteins and peptides has attracted a
lot of attention in biomedical applications. Hence, fundamental and experimental estimation …

Using implicit-solvent potentials to extract water contributions to enthalpy–entropy compensation in biomolecular associations

S Chen, ZG Wang - The Journal of Physical Chemistry B, 2023 - ACS Publications
Biomolecular assembly typically exhibits enthalpy–entropy compensation (EEC) behavior
whose molecular origin remains a long-standing puzzle. While water restructuring is …

Effect of heating and ionic strength on the interaction of bovine serum albumin and the antinutrients tannic and phytic acids, and its influence on in vitro protein …

E Kaspchak, LI Mafra, MR Mafra - Food chemistry, 2018 - Elsevier
Bioavailability of food nutrients can be reduced in the presence of antinutrients such as
phytates and tannins. This work aimed to study bovine serum albumin binding to phytic acid …

AutoDock-GIST: Incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking

S Uehara, S Tanaka - Molecules, 2016 - mdpi.com
Water plays a significant role in the binding process between protein and ligand. However,
the thermodynamics of water molecules are often underestimated, or even ignored, in …

Characterizing protein protonation microstates using Monte Carlo sampling

U Khaniya, J Mao, RJ Wei… - The Journal of Physical …, 2022 - ACS Publications
Proteins are polyelectrolytes with acidic and basic amino acids Asp, Glu, Arg, Lys, and His,
making up≈ 25% of the residues. The protonation state of residues, cofactors, and ligands …