Table 3 Common virtual screening softwares overview
From: In silico approach in reveal traditional medicine plants pharmacological material basis
Softwares | Websites | Features | References |
|---|---|---|---|
Molecular docking | |||
 Affinity | Based on simulated annealing, molecular mechanics and molecular dynamics simulation of molecular pairs of procedures, the calculation is more accurate | [44] | |
 AutoDock | Famous molecular docking program developed by the Scripps Institute. Which is one of the most widely used docking software | [44] | |
 DOCK | One of the most widely used molecular docking programs, free open access | [45] | |
 DockVision | A set of docking applets that support multiple algorithms | [46] | |
 DockIt | Provide Energy, PLP and PMF evaluation methods | [47] | |
 eHiTS | eHiTS is an exhaustive flexible-docking method that systematically covers the part of the conformational and positional search space that avoids severe steric clashes, producing highly accurate docking poses at a speed practical for virtual high-throughput screening | [48] | |
 FlexX | The method can be used in the design process of specific protein ligands. It combines an appropriate model of the physico-chemical properties of the docked molecules with efficient methods for sampling the conformational space of the ligand | [49] | |
 Glide | Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses | [50] | |
 GoldDock | GOLD is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding. Numerous enhancements and modifications have been applied to the original technique resulting in a substantial increase in the reliability and the applicability of the algorithm | [51] | |
 SystemsDock | SystemsDock is a web server for network pharmacology-based prediction and analysis, which applies high-precision docking simulation and molecular pathway map to comprehensively characterize the ligand selectivity and to illustrate how a ligand acts on a complex molecular network | [52] | |
 ZDOCK | Protein–Protein docking procedure based on geometric matching. With a goal of providing an accessible and intuitive interface, ZDOCK provide options for users to guide the scoring and the selection of output models, in addition to dynamic visualization of input structures and output docking models | [53] | |
Pharmacophore model | |||
 Apex-3D | Activity prediction expert system with 3D-QSAR. pharmacophore identification based on logical structure analysis | [54] | |
 DISCOtech | Distance comparison technique provide multi-drug group model for database search, auto recognize the priority | [55] | |
 Discovery Studio | Powerful pharmacophore identification and database search software | [56] | |
 GASP | Based on genetic algorithm to realize flexible stacking between drug molecules | [57] | |
 SEAware | Chemically similar drugs often bind to biologically diverse targets, making it difficult to predict what off-target effects a drug might have by protein structure or sequence alone. The similarity ensemble approach (SEA) addresses this problem using a different strategy; it groups receptors according to the chemical similarity of their ligands, and can identify unknown relationships between ligands and receptors amenable to experimental testing | [58] | |
Small molecule shape similarity | |||
 CerberuS |  | CerBeruS is a method developed for iterative screening. CerBeruS is based on Daylight fingerprints. CerBeruS proposes only highly similar molecules for testing. This strategy results in a high hit rate but is unlikely to identify new scaffolds or lead series | [59] |
 FlexS | FlexS is an incremental construction procedure. The molecules to be superimposed are partitioned into fragments. Starting with placements of a selected anchor fragment, computed by two alternative approaches, the remaining fragments are added iteratively. At each step, flexibility is considered by allowing the respective added fragment to adopt a discrete set of conformations. The mean computing time per test case is about 1:30 min on a common-day workstation | [60] | |
 BRUTUS |  | BRUTUS aligns molecules using field information derived from charge distributions and van der Waals shapes of the compounds. Molecules can have similar biological properties if their charge distributions and shapes are similar, even though they have different chemical structures; that is, BRUTUS can identify compounds possessing similar properties, regardless of their structures | [61] |
 WEGA | (WEGA), is proposed to improve the accuracy of the first order approximation. The new approach significantly improves the accuracy of molecular volumes and reduces the error of shape similarity calculations by 37% using the hard-sphere model as the reference. The new algorithm also keeps the simplicity and efficiency of the FOGA (First Order Gaussian Approximation) | [62] | |