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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
TLDR
The results show that ensemble docking successfully predicts the binding modes of the inhibitors, and discriminates the inhibitors from a set of noninhibitors with similar chemical properties. Expand
An iterative knowledge‐based scoring function for protein–protein recognition
TLDR
A distance‐dependent knowledge‐based scoring function to predict protein–protein interactions and the binding scores predicted by ITScore‐PP correlated well with the experimentally determined binding affinities, yielding a correlation coefficient of R = 0.71. Expand
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.
TLDR
Three basic types of scoring functions (force-field, empirical, and knowledge-based) and the consensus scoring technique that are used for protein-ligand docking are reviewed and a discussion of the challenges faced by existing scoring functions and possible future directions for developing improved scoring functions is discussed. Expand
A chemical genetic approach demonstrates that MPK3/MPK6 activation and NADPH oxidase-mediated oxidative burst are two independent signaling events in plant immunity.
TLDR
The establishment of an mpk3 mpk6 double mutant system using a chemical genetic approach provides a powerful tool to investigate the function of MPK3/MPK6 in the plant defense signaling pathway. Expand
The Two ATP Binding Sites of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Play Distinct Roles in Gating Kinetics and Energetics
TLDR
Based on the crystal structures of NBDs, sequence alignment, and homology modeling, two critical aromatic amino acids are identified that coordinate the adenine ring of the bound ATP and suggest distinct roles of these two ATP binding sites in channel opening. Expand
Ion sensing in the RCK1 domain of BK channels
TLDR
Experimental results and molecular modeling suggest that the binding of Ca2+ by the side chains of E535 and the previously identified D367 changes the conformation around the binding site and turns the side chain of M513 into a hydrophobic core, providing a basis to understand howCa2+ binding at this site opens the activation gate of the channel that is remotely located in the membrane. Expand
Advances and Challenges in Protein-Ligand Docking
TLDR
Recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking are reviewed. Expand
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
Accounting for the effect of solvent on the strength of molecular interactions has been a long-standing problem for molecular calculations in general and for structure-based drug design inExpand
Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.
TLDR
This work substantially truncates A9, an RNA aptamer to prostate-specific membrane antigen (PSMA), which retains binding activity, functionality, and is amenable to large-scale chemical synthesis for future clinical applications and highlights the utility of existing RNA structural prediction and protein docking techniques that may be generally applicable to developing RNA aptamers optimized for therapeutic use. Expand
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
TLDR
A number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments are generated, suggesting that there may be important physical chemistry missing in the energy calculations. Expand
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