WaterKit: thermodynamic profiling of protein hydration sites

Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the last decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models), to more computationally expensive and accurate ones mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well suited to be integrated in high-throughput pipelines such as molecular docking

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

AutoDock Vina is arguably one of the fastest and most widely used open-source docking engines. However, compared to other docking engines in the AutoDock Suite, it lacks features that support modeling of specific systems such as macrocycles or modeling water explicitly. Here, we describe the implementation of these functionality in AutoDock Vina 1.2.0. Additionally, AutoDock Vina 1.2.0 supports the AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Furthermore, we implemented Python bindings to facilitate scripting and the development of docking workflows. This work is an effort toward the unification of the features of the AutoDock4 and AutoDock Vina docking engines. The source code is available at https://github.com/ccsb-scripps/AutoDock-Vina</pre

Apical surgery of a maxillary molar creating a maxillary sinus window using ultrasonics: a clinical case

AIM: To describe a method of carrying out apical surgery of a maxillary molar using ultrasonics to create a lateral sinus window into the maxillary sinus and an endoscope to enhance visibility during surgery. SUMMARY: A 37-year-old female patient presented with tenderness to percussion of the maxillary second right molar. Root canal treatment had been undertaken, and the tooth restored with a metal-ceramic crown. Radiological examination revealed an apical radiolucency in close proximity to the maxillary sinus. Apical surgery of the molar was performed through the maxillary sinus, using ultrasonics for the osteotomy, creating a window in the lateral wall of the maxillary sinus. During surgery, the lining of the sinus was exposed and elevated without perforation. The root-end was resected using a round tungsten carbide drill, and the root-end cavity was prepared with ultrasonic retrotips. Root-end filling was accomplished with MTA(®) . An endoscope was used to examine the cut root face, the prepared cavity and the root-end filling. No intraoperative or postoperative complications were observed. At the 12-month follow-up, the tooth had no clinical signs or symptoms, and the radiograph demonstrated progressing resolution of the radiolucency. KEY LEARNING POINTS: When conventional root canal retreatment cannot be performed or has failed, apical surgery may be considered, even in maxillary molars with roots in close proximity to the maxillary sinus. Ultrasonic sinus window preparation allows more control and can minimize perforation of the sinus membrane when compared with conventional rotary drilling techniques. The endoscope enhances visibility during endodontic surgery, thus improving the quality of the case

New prediction categories in CASP15

Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments change with the need to address specific problems in structure modeling. In CASP15, four new prediction categories were introduced: RNA structure, ligand-protein complexes, accuracy of oligomeric structures and their interfaces, and ensembles of alternative conformations. This paper lists technical specifications for these categories and describes their integration in the CASP data management system