BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures.

Molecular docking serves as an important tool in modeling protein-ligand interactions. However, it is still challenging to incorporate overall recepto...
3MB Sizes 0 Downloads 0 Views

Recommend Documents


Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.
Proteins play an important role in biological processes in living organisms. Many protein functions are based on interaction with other proteins. The structural information is important for adequate description of these interactions. Sets of protein

Energy Minimization on Manifolds for Docking Flexible Molecules.
In this paper, we extend a recently introduced rigid body minimization algorithm, defined on manifolds, to the problem of minimizing the energy of interacting flexible molecules. The goal is to integrate moving the ligand in six dimensional rotationa

Exploring the interactions between isoprenoid chain and labdenediol diphosphate synthase based on molecular docking and quartz crystal microbalance.
Many natural products and biosynthetic intermediates contain isoprenoid chains. Isoprenoid chains are believed to interact with some proteins in the biological systems, but such interactions remain poorly understood. Here labdenediol diphosphate synt

A new configurational bias scheme for sampling supramolecular structures.
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siep

Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: a comprehensive quantum chemical approach.
The study aimed to cast light on the structure and internal energetics of guanine- and xanthine-based model DNA quadruplexes and the physico-chemical nature of the non-covalent interactions involved. Several independent approaches were used for this

Structure-based cross-docking analysis of antibody-antigen interactions.
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cros

A privacy authentication scheme based on cloud for medical environment.
With the rapid development of the information technology, the health care technologies already became matured. Such as electronic medical records that can be easily stored. However, how to get medical resources more convenient is currently concerning

deepTools: a flexible platform for exploring deep-sequencing data.
We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to e

Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM.
Protein-ligand docking is a commonly used method for lead identification and refinement. While traditional structure-based docking methods represent the receptor as a rigid body, recent developments have been moving toward the inclusion of protein fl

POSIT: Flexible Shape-Guided Docking For Pose Prediction.
We present a new approach to structure-based drug design (POSIT) rigorously built on the simple concept that pose prediction is intimately coupled to the quality and availability of experimental structural data. We demonstrate the feasibility of the