The role of water in protein-DNA recognition

B Jayaram, T Jain - Annu. Rev. Biophys. Biomol. Struct., 2004 - annualreviews.org
▪ Abstract Is it by design or by default that water molecules are observed at the interfaces of
some protein-DNA complexes? Both experimental and theoretical studies on the …

Plasmepsins as potential targets for new antimalarial therapy

K Ersmark, B Samuelsson… - Medicinal research …, 2006 - Wiley Online Library
Malaria is one of the major diseases in the world. Due to the rapid spread of parasite
resistance to available antimalarial drugs there is an urgent need for new antimalarials with …

Ligand− protein docking with water molecules

BC Roberts, RL Mancera - Journal of chemical information and …, 2008 - ACS Publications
The presence of water molecules plays an important role in the accuracy of ligand− protein
docking predictions. Comprehensive docking simulations have been performed on a large …

Accounting for water molecules in drug design

SE Wong, FC Lightstone - Expert opinion on drug discovery, 2011 - Taylor & Francis
Importance of the field: Water molecules often appear around ligands in protein crystal
structures. Reliable prediction of the effects of water on ligand binding remains a challenge …

3dSS: 3D structural superposition

K Sumathi, P Ananthalakshmi… - Nucleic Acids …, 2006 - academic.oup.com
Abstract 3dSS is a web-based interactive computing server, primarily designed to aid
researchers, to superpose two or several 3D protein structures. In addition, the server can be …

Ligand− protein cross-docking with water molecules

R Thilagavathi, RL Mancera - Journal of chemical information and …, 2010 - ACS Publications
The accuracy of ligand− protein docking may be affected by the presence of water
molecules on the surface of the protein. Cross-docking simulations have been performed on …

Structural studies of Myceliophthora Thermophila Laccase in the presence of deep eutectic solvents

JC Chan, B Zhang, M Martinez, B Kuruba… - Enzyme and Microbial …, 2021 - Elsevier
In this work, we elucidated the interactions between Myceliophthora thermophila laccase
and deep eutectic solvent (DES) by crystallographic and kinetics analyses. Four types of …

[HTML][HTML] Functional plasticity in the substrate binding site of β-secretase

AA Gorfe, A Caflisch - Structure, 2005 - cell.com
The aspartic protease β-secretase (BACE) cleaves the amyloid precursor protein into a 42
residue β-peptide, which is the principal biochemical marker of Alzheimer's disease. Multiple …

Conformational dynamics and binding free energies of inhibitors of BACE-1: from the perspective of protonation equilibria

MO Kim, PG Blachly… - PLoS computational …, 2015 - journals.plos.org
BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer's
disease, catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner. The catalytic …

The role of conserved water molecules in the catalytic domain of protein kinases

JDR Knight, D Hamelberg… - Proteins: Structure …, 2009 - Wiley Online Library
Protein kinases are essential signaling molecules with a characteristic bilobal shape that
has been studied for over 15 years. Despite the number of crystal structures available, little …