The hydrophobic effect revisited—studies with supramolecular complexes imply high‐energy water as a noncovalent driving force

F Biedermann, WM Nau… - Angewandte Chemie …, 2014 - Wiley Online Library
Traditional descriptions of the hydrophobic effect on the basis of entropic arguments or the
calculation of solvent‐occupied surfaces must be questioned in view of new results obtained …

Effects of molecular crowding on the structures, interactions, and functions of nucleic acids

S Nakano, D Miyoshi, N Sugimoto - Chemical reviews, 2014 - ACS Publications
Nucleic acids are excellent at recognizing complementary sequences through the formation
of Watson− Crick base pairs. Since the base pairing enables the highly selective …

Water mediation in protein folding and molecular recognition

Y Levy, JN Onuchic - Annu. Rev. Biophys. Biomol. Struct., 2006 - annualreviews.org
Water is essential for life in many ways, and without it biomolecules might no longer truly be
biomolecules. In particular, water is important to the structure, stability, dynamics, and …

Protein–DNA binding: complexities and multi-protein codes

T Siggers, R Gordân - Nucleic acids research, 2014 - academic.oup.com
Binding of proteins to particular DNA sites across the genome is a primary determinant of
specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded …

DNA's chiral spine of hydration

ML McDermott, H Vanselous, SA Corcelli… - ACS central …, 2017 - ACS Publications
The iconic helical structure of DNA is stabilized by the solvation environment, where a
change in the hydration state can lead to dramatic changes to the DNA structure. X-ray …

RRM–RNA recognition: NMR or crystallography… and new findings

GM Daubner, A Cléry, FHT Allain - Current opinion in structural biology, 2013 - Elsevier
To characterize protein–RNA recognition at the molecular level, structural biology has
turned out to be an indispensable approach. Detailed and direct insights into the mechanism …

Cre recombinase and other tyrosine recombinases

G Meinke, A Bohm, J Hauber, MT Pisabarro… - Chemical …, 2016 - ACS Publications
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the
predictable modification of genomes as they enable precise genome editing in heterologous …

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 …

Water structure and interactions with protein surfaces

TM Raschke - Current opinion in structural biology, 2006 - Elsevier
The structure of liquid water and its interaction with biological molecules is a very active area
of experimental and theoretical research. The chemically complex surfaces of protein …

AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors

T Singh, D Biswas, B Jayaram - Journal of chemical information …, 2011 - ACS Publications
We report here a robust automated active site detection, docking, and scoring (AADS)
protocol for proteins with known structures. The active site finder identifies all cavities in a …