IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface

نویسندگان

  • Yin Xue Sun
  • Yan Xin Huang
  • Feng Li Li
  • Hong Yan Wang
  • Cong Fan
  • Yong Li Bao
  • Lu Guo Sun
  • Zhi Qiang Ma
  • Jun Kong
  • Yu Xin Li
چکیده

BACKGROUND The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. RESULTS A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. CONCLUSIONS IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters

BACKGROUND Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is avai...

متن کامل

VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface

A graphical user interface (GUI) for our previously published virtual screening (VS) and data management platform VSDMIP (Gil-Redondo et al. J Comput Aided Mol Design, 23:171-184, 2009) that has been developed as a plugin for the popular molecular visualization program PyMOL is presented. In addition, a ligand-based VS module (LBVS) has been implemented that complements the already existing str...

متن کامل

Using a Virtual Reality Environment to Simulate the Pushing of Cylindrical Nanoparticles

With the rise in the use of AFM (Atomic Force Microscope), we have witnessed a growing use of atomic microscope based nanorobots in the precise displacement of various particles. There are certain limitations to the application of nanorobots in the moving of nanoparticles. One of the most important of these limitations is the lack of an appropriate image feedback concurrent with the displaci...

متن کامل

iDrug: a web-accessible and interactive drug discovery and design platform

BACKGROUND The progress in computer-aided drug design (CADD) approaches over the past decades accelerated the early-stage pharmaceutical research. Many powerful standalone tools for CADD have been developed in academia. As programs are developed by various research groups, a consistent user-friendly online graphical working environment, combining computational techniques such as pharmacophore m...

متن کامل

ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

BACKGROUND Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attemp...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره 6  شماره 

صفحات  -

تاریخ انتشار 2012