Virtual Computational Chemistry Laboratory – Design and Description

By Igor V. Tetko, J. Gasteiger, Roberto Todeschini, A. Mauri, D. Livingstone, Peter Ertl, V. Palyulin, E. Radchenko, N. Zefirov, A. Makarenko and 2 more. 2005

1,460 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy

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Citations in the corpus

Mordred: a molecular descriptor calculator (2018, methodology): “It can calculate numerous descriptors, and it has several interfaces, such as a GUI, CLI, web (e-Dragon [23], which is based on an older free version of Dragon), and KNIME.”
Open Babel: An open chemical toolbox (2011, neutral): “VCCLAB Virtual Computational Chemistry Laboratory [107] http://www.”
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies (2019, methodology): “These software packages include docking software such as AutoDock Vina [63], Glide [64, 65], ICM [66], Corina [67], Gold [68], Cactvs [69], Rosetta [70], and EFindSite [71], and ligand preparation software such as Brikard [72], RDKit [48], Open Babel [73] and Maestro [74].”
Artificial intelligence to deep learning: machine intelligence approach for drug discovery (2021, background): “…r ong p r e d i c ti v e po w e r o f D ee p D r ug [ 420 ] vcclab. org/ lab/ pclie nt/) [304], E-DRAGON (http:// www. vcclab. org/ lab/ edrag on/) [304], ChemSpider (http:// www. chems pider. com/) [306], SPARC (http:// sparc. chem. uga. edu/ sparc/) [307], and OSIRIS property explorer (https://…”
ChemMine tools: an online service for analyzing and clustering small molecules (2011, background): “For instance, ChemDB and VCCLab (13,43) can be used for property predictions and structure format interconversions of single compound queries; and PubChem supports structure-based clustering for compounds retrieved from its own database.”
DRAGON SOFTWARE: AN EASY APPROACH TO MOLECULAR DESCRIPTOR CALCULATIONS (2006, methodology): “E-DRAGON [4] uses a Java applet which employs DRAGON in order to calculate the molecular descriptors directly within an HTML page.”
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery (2011, methodology): “The retrieved QSAR model page (Figure 3) contains the information about target and ID, target species, chemical type, compound mode of action, QSAR models, the molecular descriptors in the QSAR models, references and hyperlinks to the molecular descriptor computation web servers MoDeL (32) and e-dra”
Control of plant diseases by natural products: Allicin from garlic as a case study (2008, background): “The use of garlic preparations or allicin against plant pathogens has already been documented (Arya et al. 1995; Bianchi et al. 1997; Cao and vanBruggen 2001; Russell and Mussa 1977 ) and there are several preparations based on garlic compounds available commercially, although the latter are primar”
Ligand Pose and Orientational Sampling in Molecular Docking (2013, methodology): “CORINA[127] is used to produce an initial 3D conformation from input SMILES, AMSOL is used to compute partial charges and ligand desolvation terms[116], and OMEGA[83,105] is used to enumerate multiple 3D conformations.”
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database (2018, background): “VCCLAB [46] Free Yes Number: 14 Contents: B (Dif‐ ferent LogP, LogS and pKa from different theories) No No No No No”
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information (2011, methodology): “Other online tools (e.g., VCCLAB [13], OpenTox [14], ChemBench [15], QSAR DataBank [16]) provide modeling facilities but lack an integration with a chemical database and, therefore, cannot support a typical workﬂow of QSAR/QSPR research.”