Target fishing often relies on the use of reverse docking to identify potential target proteins of ligands from protein database. The limitation of reverse docking is the accuracy of current scoring funtions used to distinguish true target from non-target proteins. Many contemporary scoring functions are designed for the virtual screening of small molecules without special optimization for reve...

LAI-YUEN, SUSANA KARINA. Nano-scale Molecular Docking and Assembly Simulator (NanoDAS) with Haptic Force-Torque Rendering and Energy Minimization for ComputerAided Molecular Design (CAMD). (Under the direction of Dr. Yuan-Shin Lee). The objective of this research is to investigate and develop computational and haptic interface techniques to improve the search and design of molecular docking, an...

UNLABELLED A protein-protein docking decoy set is built for the Dockground unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies. AVAILABILITY The decoys...

In recent years, the importance of considering induced fit effects in molecular docking calculations has been widely recognised in the molecular modelling community. While small-scale protein side-chain movements are now accounted for in many state-of-the-art docking strategies, the explicit modelling of large-scale protein motions such as loop movements in kinase domains is still a challenging...

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...

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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...