Unlock your biological data


Try: RNA sequencing CRISPR Genomic databases DESeq

1 - 50 of 176 results
filter_list Filters
healing Disease
settings_input_component Operating System
tv Interface
computer Computer Skill
copyright License
1 - 50 of 176 results
UCSF Chimera
star_border star_border star_border star_border star_border
star star star star star
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.
Allows users to access and preprocess structural data for all kinds of life science research, and gives an immediate visual impression of the overall protein structure and contained ligand molecules. ProteinPlus contains a server for special interest to life scientists with an occasional need to work with protein structures thanks to six services addressing the most important tasks at the beginning of structure analysis (Protoss; PoseView; EDIA; SIENA; DoGSiteScorer; HyPPI). Users can choose an application service of interest, set additional tool configurations and start the calculation.
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.
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.
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.
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.
AMMOS / Automatic Molecular Mechanics Optimization for in silico Screening
Treats of efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 web server aims to providing at the scientific community a free and user-friendly protein-ligand-water minimization tool. It offers the possibility for users to refine a large number of protein-ligand complexes after virtual screening. This tool proposes several solutions to assist docking and structure-based virtual screening experiments keeping in mind that water molecules mediating protein-ligand interactions are of key importance to design high-affinity hit molecules.
A web server dedicated to the docking of small molecules on target proteins. SwissDock aims at extending the use of protein-small molecule docking software far beyond experts in the field by providing convenient answers to many of the difficulties mentioned above. Predicted binding modes (BMs) can be viewed online with a simple embedded applet or analyzed in more details thanks to a seamless integration with the UCSF Chimera molecular viewer. The automatic setup of protein and ligand structures, the different parameter presets and the convenient visualization and analysis of docking predictions makes it accessible to a wide audience.
IC50-to-Ki converter
Converts g IC50 to Ki values for inhibitors of enzymes and of protein-ligand interactions. IC50-to-Ki converter is a web server that calculates Ki values from IC50 values using equations for enzyme-substrate and target-ligand interactions by different inhibitory mechanisms. The software provides results for classic and tight-binding inhibitors of enzyme activity and ligand-binding reactions that are assumed to follow relatively simple kinetic schemes. It aims to facilitate research and the development of potential therapeutic products.
PLIP / Protein-Ligand Interaction Profiler
A web service for fully automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures. PLIP stands out by offering publication-ready images, PyMOL session files to generate custom images and parsable result files to facilitate successive data processing. Furthermore, the availability of PLIP source code enables local batch processing, customization of the algorithm for special applications as well as active development of the tool in the community.
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.
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.
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.
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.
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.
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.
PL-PatchSurfer / Protein-Ligand PatchSurfer
Evaluates protein-ligand interactions based on compatibility of local molecular surfaces. PL-PatchSurfer is a structure-based virtual screening (SBVS) program that ranks ligands in a library for a target pocket by identifying complementarity between pocket and ligand local surface regions. The software uses a molecular surface representation. It can extend the capability of virtual screening by providing accurate predictions in difficult cases, such as scaffold hopping or cases where only apo form of targets or template-based models of targets are available.
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.
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.
PLATINUM / Protein–Ligand ATtractions Investigation NUMerically
A web app designed for analysis and visualization of hydrophobic/hydrophilic properties of biomolecules supplied as 3D-structures. Furthermore, PLATINUM provides a number of tools for quantitative characterization of the hydrophobic/hydrophilic match in biomolecular complexes e.g. in docking poses. These complement standard scoring functions. The calculations are based on the concept of empirical molecular hydrophobicity potential (MHP).
0 - 0 of 0 results
1 - 13 of 13 results
filter_list Filters
computer Job seeker
Disable 4
person Position
thumb_up Fields of Interest
public Country
language Programming Language
1 - 13 of 13 results