RosettaDock has been increasingly used in protein docking and design strategies in order to predict the structure of protein-protein interfaces. Here we test capabilities of RosettaDock 3.2, part of the newly developed Rosetta v3.2 modeling suite, against Docking Benchmark 3.0, and compare it with RosettaDock v2.3, the latest version of the previous Rosetta software package. The benchmark conta...

The existence of vesicular docking sites in central synapses is supported by morphological and biochemical evidence, but their functional role remains elusive. To investigate this role we have studied single depressing GABAergic synapses where multivesicular release and postsynaptic receptor saturation have been documented. We used failure/success patterns to estimate the number of vesicular do...

Contents 1. Introduction 1 1.

Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs). MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation ...

This paper provides a literature review of docking research, an area that has relatively few research articles as compared to generic automatic guided vehicle (AGV) or mobile robot research. Docking refers to the arrival and stopping at a position relative to another object. Docking can include positioning the vehicle or the equipment onboard the vehicle relative to another object, for example ...

Docking functions are believed to be the essential component of docking algorithms. Both physically and statistically based functions have been proposed, but there is no consensus about their relative performances. Here, we propose an evaluation approach based on exhaustive enumeration of all possible docking solutions obtained with a discretized description of a rigid docking process. We apply...

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, ...

Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We discuss the peculiarities of protein-carbohydrate interactions and their impact on protein-carbohydrate docking and review the state of the art in docking of...

Autonomous underwater vehicles (AUVs) have been deployed for underwater exploration. However, its potential is confined by its limited on-board battery energy and data storage capacity. This problem has been addressed using docking systems by underwater recharging and data transfer for AUVs. In this work, we propose a vision based framework for underwater docking following these systems. The pr...

BACKGROUND Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come wit...