The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the “correct” native conformation within the list of predicted docked conformations signals a near solution to the docking pr...

BACKGROUND Ulnar collateral ligament reconstruction (UCLR) has become a common procedure performed in overhead-throwing athletes of many athletic levels. PURPOSE/HYPOTHESIS The purpose of this study was to determine whether clinical outcomes and return-to-sport (RTS) rates differ among patients undergoing UCLR based on graft choice, surgical technique, athletic competition level, handedness, ...

The Monterey Bay Aquarium Research Institute (MBARI) has developed a 21-inch (54 cm) diameter docking AUV and companion docking station. This program resulted in four consecutive successful autonomous homing and docking events in the open ocean, which included downloading data, uploading a new mission plan, recharging the battery, and complete power cycling of the AUV. We describe the design, s...

Acetylcholinesterase (AChE) enzyme which catalyses the hydrolysis of choline esters, such as acetylcholine, is very important in nerve function. Previous structural studies showed the possible amyloid fibril formation on the AChE. Therefore it is important to understand interaction of ligands to prevent the formation of  amyloid fibrils. The purpose of the present study was to  char...

Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and bench...

Docking and fusion of transport vesicles constitute elementary steps in intracellular membrane traffic. While docking is thought to be initiated by Rab-effector complexes, fusion is mediated by SNARE (N-ethylmaleimide-sensitive factor [NSF] attachment receptor) proteins. However, it has been recently debated whether SNAREs also play a role in the establishment or maintenance of a stably docked ...

Molecular docking programs play a crucial role in drug design and development. In recent years, much attention has been devoted to the protein-peptide docking problem in which docking of a flexible peptide with a known protein is sought. In this work we present a new docking algorithm which is based on the use of a filling function method for continuos constrained global optimization. Indeed, t...

In the last years, the importance of water molecules in pose prediction experiments has been widely recognized and several approaches to integrate water molecules into the docking process have been proposed [1,2]. The inclusion of water molecules extends the classical two-body problem of docking a flexible ligand into a protein receptor to a multi-body docking problem as protein-ligand, protein...

The goal of this work was to determine if it is feasible to use Mir/Shuttle docking data to perform Mir damage detection. A time-domain technique called a Remote Sensing System was proposed as an approach. The method uses inverse structural dynamics to identify physical characteristics of a structure which can subsequently be used for damage detection. The RSS method was demonstrated for a nume...