VSDMIP: virtual screening data management on an integrated platform

Abstract

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

Challenges and advances in computational docking: 2009 in review

“…Other advancements in automation of virtual screening include the development of integrated computational platforms, such as Virtual Screening Data Management on an Integrated Platform (VSDMIP) (130).…”

Mechanistic Insight into the Catalytic Activity of ββα‐Metallonucleases from Computer Simulations: Vibrio vulnificus Periplasmic Nuclease as a Test Case

“…Ligand docking: The CGRID and CDOCK programs, [43] as implemented in the VSDMIP platform, [44] were used to dock the minimal substrate deoxythymidine 3',5'-bis-(p-nitrophenylphosphate) into the active site of Vvn, as found in PDB entry 1OUO. [6] …”

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

“…Mean values and standard deviations are also reported. SBVS was performed by the combined use of CGRID and CDOCK [25] as explained in the original VSDMIP publication [15]. Briefly: Finally, LBVS was employed prior to SBVS to illustrate the connection between both modules and also to test its ability as a filter to reduce docking times using ACE and MR as the targets.…”

“…Furthermore, other implementations are accessible through a web server (DOCKBLAST [12]), distributed over a grid [13], or endowed with database capabilities [14]. In our lab, VSDMIP [15] was developed to provide the scientific community with a flexible, fully automated computational platform to perform VS experiments and manage every piece of data in an integrated fashion. Significant advantages of this platform are its underlying database, which stores ligand information and every result arising from the different steps of a given VS protocol, and its modular and pluggable architecture, which allows customization of each step of the procedure.…”