The binding of small molecule ligands to large protein targets is central to numerous biological processes. The accurate prediction of the binding modes between the ligand and protein, (the docking problem) is of fundamental importance in modern structure-based drug design. An overview of current docking techniques is presented with a description of applications including single docking experim...

BACKGROUND This paper presents an overview of the global controversies surrounding cosmetic tail docking in puppies, some observed inconsistent practices among dog breeders and Veterinarians in West Africa, and the need for the African Veterinary Profession to take a decisive position on the cosmetic docking procedure. CASE PRESENTATION An interesting report of observed complications associat...

Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and...

Most docking methods involving a small robot and a station require the docking station to communicate with the robot. Few robots are able to dock with a passive base station. Even fewer can also be “driven” by a bird. This paper presents a novel way for parrot-guided transportation and autonomous docking using range lights and a web camera.

Traditional approaches to protein-protein docking sample the binding modes with no regard to similar experimentally determined structures (templates) of protein-protein complexes. Emerging template-based docking approaches utilize such similar complexes to determine the docking predictions. The docking problem assumes the knowledge of the participating proteins' structures. Thus, it provides th...

We describe a novel method for predicting protein docking conformations using spectral analysis techniques. Rigid-body docking methods based on shape complementarity, particularly Fourier transform based techniques are successful for docking monomers with conformations adopted at binding (complexed conformations) [4]. This approach is very efficient because a complete search over all six degree...

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Membrane-membrane recognition and binding are crucial in many biological processes. We report an approach to studying the dynamics of such reactions by using DNA-tethered vesicles as a general scaffold for displaying membrane components. This system was used to characterize the docking reaction between two populations of tethered vesicles that display complementary DNA. Deposition of vesicles o...

Molecular docking is a widely used method for lead optimization. However, docking tools often fail to predict how a ligand (the smaller molecule, such as a substrate or drug candidate) binds to a receptor (the accepting part of a protein). We present here the HarmonyDOCK, a novel method for assessing the docking software accuracy, and creating the scoring function which would determine consensu...

Before exocytosis, vesicles must first become docked to the plasma membrane. The SNARE complex was originally hypothesized to mediate both the docking and fusion steps in the secretory pathway, but previous electron microscopy (EM) studies indicated that the vesicular SNARE protein synaptobrevin (syb) was dispensable for docking. In this paper, we studied the function of syb in the docking of l...