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A package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Glide offers the full range of quick and accurate options, from the HTVS to the SP. It also provides virtual screening, accurate binding mode prediction and universal applicability. Comparisons to published data on RMS deviations show that Glide is nearly twice as accurate as GOLD and more than twice compared to FlexX. Glide is also found to be more accurate than the Surflex method.

VMD / Visual Molecular Dynamics

Displays molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities. VMD has been developed for interactive graphical display of molecular systems, in particular biopolymers such as proteins or nucleic acids. A key feature in VMD is the abilily to work with molecular dynamics simulation programs, and to display the simulated molecule am its motion is computed VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs.

UCSF Chimera

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Permits to interactively visualize and analyse molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. UCSF Chimera allows users to incorporate new features. It contains some extensions which permits to visualize large-scale molecular assemblies such as viral coats, and allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions can be used for extend the tool capabilities.

AutoDock Vina

Allows molecular docking and virtual screening. AutoDock Vina is one of the two generations of distributions of AutoDock. This software uses a sophisticated gradient optimization method in its local optimization procedure. The calculation of the gradient effectively gives the optimization algorithm a “sense of direction” from a single evaluation. By using multithreading, this software can further speed up the execution by taking advantage of multiple CPUs or CPU cores.


Offers solution for pharmacophore perception, quantitative structure-activity relationship (QSAR) model development, and 3D database screening. PHASE aims to suggest a set of plausible models that can be evaluated by various criteria whose relevance is assessed by the user. It is able to reproduce crystallographic pharmacophores. The tool extracts orthogonal latent factors from a data matrix by using a standard recursive procedure. It can efficiently classify a large test set of inhibitors into three activity categories.


Allows flexible ligand docking. Idock is a virtual screening tool that consists of two basic components: a scoring function to predict the binding affinity, and an optimization algorithm to explore the conformational space. The software has built-in support for virtual screening, searches for ligands in a user-specified folder and docks them one by one. It also reuses threads and grid maps across multiple ligands. It is capable of screening 1.3 drug-like ligands per CPU minute on average.


Studies large virtual libraries of electrophilic small molecules. DOCKovalent exhaustively samples all poses and ligand conformations with respect to the covalent bond to the target nucleophile, constrained by ideal bond lengths and angles. DOCKovalent was used to prospectively screen compound libraries against three targets of therapeutic interest: AmpC β-lactamase, RSK2 kinase and JAK3 kinase. Multiple potent, reversible covalent inhibitors were found against all three targets. X-ray crystal structures of predicted ligands, and the occasional false negative, illuminated not only the method’s ability to prospectively identify ligands and to predict their structures, but also its limitations. Several of the new covalent ligands were tested in cell culture experiments that established biological efficacy and target engagement. To ensure that the method may be used by a broad community, it has been made available on an easy to use web server.


Automatically generates 2D ligand-protein interaction diagrams. LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs. The software allows the 2D representation of multiple ligand protein complexes in a simple and automated manner, without the need of prealigning the protein structure components or using 3D viewers. It enables the direct comparison of multiple, related protein complexes, while allowing for the simultaneous variation of both protein sequence and compound formula.


Allows analysis of the structural variability landscape for a given protein. SA-conf is a structural alphabet (SA)-based tool that facilitates the analysis and comparison of large and diverse multiple target conformations (MTC) sets and exploration of available structural variability landscape associated with a given target. The software can detect putative structural deformation induced by a partner binding when applied to heterogeneous MTC set as well as intrinsic variability when applied to homogeneous MTC set.

MIEC-SVM / Molecular Interaction Energy Component & Support Vector Machine

A structure-based method for predicting protein recognition specificity. To make the method more accessible to the scientific community, we construct a pipeline to facilitate the use of existing MIEC-SVM models and the construction of new ones. The pipeline is divided into three consecutive modules: complex structure building, MIEC generation and SVM training/prediction. The modular design of the program allows easy customization of the standard protocol for a particular application. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency.


Predicts binding sites of non-metal ligands. GalaxySite is a web server that employs molecular docking. Binding ligand is predicted using a similarity-based method, and the protein structure is provided by user or predicted from a template-based modeling method. The method is applicable to experimentally resolved structures, model protein structures and protein sequences. The software predicts specific binding ligands and binding poses, which can be useful for further applications, e.g. in computer-aided drug discovery.


Makes the screening of millions of compounds across entire proteomes feasible. FINDSITE(comb) is an online service. It has virtual screening accuracy better than the best docking method under the challenging condition that no templates > 30% sequence ID to the target are present in the ligand binding databases. This method does not require experimental structure to give the best performance. For average 300 AA protein, FINDSITE(comb) can screen ten million compounds within 2 days on a single computer node.


Maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein–protein, protein–nucleic acid, protein–compound, and protein–metal ion binding sites. GenProBiS enables detection of sequence variants within a protein binding site. It allows visual exploration of interactions, or loss of interactions, of a specific mis-sense mutation with a specific ligand. The tool permits focused laboratory experiments based on targeted hypotheses in several research fields including human, veterinary medicine, animal and plant breeding.


Uses a combination of stochastic and deterministic search techniques to generate low energy ligand poses. rDock generate a single ligand pose uses 3 stages of Genetic Algorithm search (GA1, GA2, GA3), followed by low temperature Monte Carlo (MC) and Simplex minimization (MIN) stages. It can recognize nine feature types: neutral hydrogen bond acceptor, neutral hydrogen bond donor, hydrophobic, hydrophobic aliphatic, hydrophobic aromatic, negatively charged, positively charged, and any heavy atom.


A web server for prediction of ligands based on detected local structural similarities in proteins. ProBiS-ligands requires a query protein structure or a query binding site, and this is first compared to proteins in the nr-PDB using the local structural alignment algorithm ProBiS, resulting in a list of similar representative protein structures that share similar 3D amino acid environments with the query protein. ProBiS-ligands provides an interactive environment in which users can explore the predicted protein–ligand complexes. One of the major advantages of ProBiS-ligands is that it allows transposition of ligands between protein structures irrespective of protein folding and with no prior knowledge of binding sites.

JADOPPT / Java based AutoDock Preparing and Processing Tool

A visual tool for analyzing and comparing multiple docking results. JADOPPT focuses on reducing the dimensionality problem by hierarchically selecting representative poses for each docked molecule. It also calculates the RMSD between the poses and automatically clusters them. JADOPPT is an alternative tool that allows highly interactive visual analysis, and provides means for refinement of docking studies. It also overcomes the limitations of single molecule analysis by employing a clustering methodological approach and allows comparisons of multiple dockings.

Rcpi / Compound-Protein Interaction with R

A freely available R/Bioconductor package for complex molecular representation from drugs, proteins and more complex interactions, including protein-protein and compound-protein interactions. Rcpi could calculate a large number of structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of small molecules from their topology and protein-protein interaction and compound-protein interaction descriptors. In addition to main functionalities, Rcpi could also provide a number of useful auxiliary utilities to facilitate the user's need.

MANORAA / Mapping Analogous Nuclei Onto Residue And Affinity

A web service for identification of ligand & residue interactions, SNP and pathway analysis. Manoraa allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time.


A web service enabling drug developers to carry out network pharmacology-based prediction and analysis by integrating results from structural biology with systems biology. Its user-friendly GUI interface simplifies essential operations for large-scale screening. Using the predictive docking approach, systemsDock can test a large number of target proteins with good prediction accuracy. This will reduce the number of tests for bioassay. Together with a curated pathway map, systemsDock helps to comprehensively characterize the underlying mechanism of a drug candidate and to interpret its cascading effects, improving the prediction of drug efficacy and safety.


Allows to evaluate protein-ligand binding. MedusaScore is a scoring function that describes the protein-ligand binding using physical interaction model. The function includes an explicit hydrogen-bonding model and EEF1 pairwise implicit solvent model, which allows accurate modeling of the hydrogen-bonding and desolvation effect without large-scale molecular dynamics (MD) simulations. Since the MedusaScore does not rely on parameter training using protein-ligand binding data, it is transferable to targets and small molecules beyond the tested datasets.

PLEIC-SVM / Protein-Ligand Empirical Interaction Components Support Vector Machine

Maps protein-ligand binding interactions on protein pocket residues. PLEIC-SVM is a classification model built as a post-docking process for virtual screening that uses active and inactive informations from a specific target for model building. The algorithm is based on the generation of the interaction matrix. It is robust in capturing important features for better virtual screening and may be useful tool ranking of actives and decoys.


Allows prediction and scoring of covalently bound ligands. CovDock is a covalent docking protocol built upon a foundation of the Glide docking algorithm and Prime structure refinement methodology for prediction of non-covalently docked poses. The software was tested with data sets aimed at addressing three common applications of docking in the context of the discovery of therapeutically valuable covalent inhibitors: pose prediction, virtual screening, and structure activity relationships (SAR) characterization. It may aid the lead optimization of covalent ligands.