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Rumex

Rumex is a genus of perennial herbs known for their edible leaves and roots.
These plants are commonly referred to as docks or sorrels, and are found throughout temperate regions of the world.
Rumex species are characterized by their distinctive leaf shapes, ranging from lanceolate to hastate, and their inconspicuous flowers that develop into dry fruits.
Many Rumex plants are valued for their medicinal properties, as well as their culinary uses in salads, soups, and other dishes.
Researchers studying Rumex face the challenge of locating the most relevant and reliable protocols from a vast body of literature.
PubCompare.ai's AI-driven platform can assist in this process, helping scientists make informed decisions by seamlessly comparing protocols and enabling typo-tolerant searches across publications, preprints, and patents.

Most cited protocols related to «Rumex»

1
ZINC Molecular Structure Generation
Catalogs are obtained
as 2D SDF files and converted to isomeric SMILES using OpenEye’s
OEChem software.19 (link) We generate up to four
stereoisomers for stereochemically ambiguous molecules. A trial 3D
structure is first generated using Molecular Networks’ Corina
program21 (link) to generate a single canonical
conformation with the best ring puckering if applicable (arguments
are -d neu, wh, rc, mc = 1, canon). Molecules are generated in four
pH ranges using Schrodinger’s Epik version 2.120922 (link) as follows. At pH of 7.05, a single best configuration
is generated using the arguments: “-ph 7.05 -ms 1”.
For the range pH of 6–8 (i.e., 7 ± 1), additional protonated
and tautomeric forms are generated such that they have a relative
population of at least 20% within that pH range using the arguments:
“ph 7.0 -pht 1.0 -tp 0.20”. Similarly for high pH of
7–9.5 (i.e., 8.75 ± 0.75) and low pH of 4.5–6 (i.e.,
5.25 ± 0.75), the arguments are “-ph 8.75 -pht 0.75 -tp
0.20” and “-ph 5.25 -pht 0.75 -tp 0.20” respectively.
For flexibase files used by DOCK 3.6,23 (link),24 (link) conformations
are calculated using OpenEye’s Omega library25 (link) with the following settings: Warts(True), FromCT(False),
FixMaxMatch(1), EnumNitrogen(false), EnumRing(false), EnergyWindow(12.5),
MaxConfGen(100000), MaxConfs(600), RMSThreshold(0.80). Atomic charges
and desolvation are calculated using AMSOL26 (link),27 (link)using a protocol we have reported previously.28 (link) The ZINC processing pipeline continues to evolve and is
described online in more detail at http://wiki.bkslab.org/index.php/ZPP.
Irwin J.J., Sterling T., Mysinger M.M., Bolstad E.S, & Coleman R.G. (2012). ZINC: A Free Tool to Discover Chemistry for Biology. Journal of Chemical Information and Modeling, 52(7), 1757-1768.
Publication 2012
Flexibase Isomerism Rumex Warts Zinc
2
Simultaneous Docking of Multiple Ligands in PDE-delta
Vina is now able to dock simultaneously multiple ligands. This functionality may find application in fragment based drug design, where small molecules that bind the same target can be grown or combined into larger compounds with potentially better affinity.
The protein PDEδ in complex with two inhibitors (PDB 5×72) (27 (link)) was used as a proof of concept to test the ability of Vina to successfully dock multiple ligands simultaneously. The two inhibitors in this structure are stereoisomers, and only the R-isomer is able to bind in a specific region of the pocket, while both the R-and S-isomers can bind to the second location. Using the Vina scoring function, the best set of poses (top 1) shows an excellent overlap with the crystallographic coordinates for one of the isomers, and reasonable overlap with the electron density for the other isomer, which shows some degree of ambiguity (Fig. 1 A). Using the AutoDock4 scoring function, similar performance in overlapping the crystallographic poses is found, but only when considering the first two sets of poses (top 2).
Johnston S.D., Lew J.E, & Berman J. (1999). Gbp1p, a Protein with RNA Recognition Motifs, Binds Single-Stranded Telomeric DNA and Changes Its Binding Specificity upon Dimerization. Molecular and Cellular Biology, 19(1), 923-933.
Publication 2021
Crystallography Electrons inhibitors Isomerism Ligands Proteins Rumex Stereoisomers
3
Protein-Protein Docking with HexServer
HexServer has an easy-to-use form-based interface, through which users may upload a pair of protein structures in PDB format. Users may optionally provide an e-mail address for notification of the status of their jobs. Figure 1 shows the web interface for defining the parameters of a docking job. For a blind unconstrained 6D docking run, it is normally sufficient to use the default values for all parameters. If the proteins to be docked have large and opposite formal charges, or if electrostatic interactions are known to be important, it is often beneficial to request a shape plus electrostatic calculation. Otherwise, a shape-only correlation is recommended.

Screenshots of the two dataentry web pages of the HexServer interface. (A) Top: the first web page is used to specify the PDB files to be uploaded, and the type of docking calculation to be performed. (B) Bottom: the second web page may be used to define optional interface residues and angular search ranges to focus the search around a known or hypothesized interface. By convention, the larger of the two proteins is called the ‘receptor’ and the smaller is called the ‘ligand,’ although Hex treats the two proteins equally. All input parameters are explained in further detail in the online Help page, and some typical protein domains are available from the ‘Examples’ page.

As described previously (11 (link)), all Hex docking correlations use SPF shape–density representations to polynomial order in order to generate very rapidly a list of up to 25 000 candidate solutions. We find that the top 3000 orientations nearly always include some near-native orientations but a larger list is used to avoid pruning good candidates in exceptional cases. These candidate solutions are then re-scored using higher order shape-only or shape plus electro-static correlations (using e.g. polynomials to order or ), as selected by the user. Requesting polynomial order (the default) gives relatively soft representations of each protein whereas order polynomials give somewhat sharper representations.
If prior information is available about one or both binding sites, the user can request that the docking search will be focused around a selected interface residue on one or both docking partners. As illustrated in Figure 1B, this is achieved by specifying one central residue from each protein to define an intermolecular axis, and by specifying two further residues to be placed on the intermolecular axis near the protein–protein interface. The user may then specify an angular search range (e.g. of 45°) for each protein with respect to the intermolecular axis in order to constrain the rotational search around the putative interface.
Macindoe G., Mavridis L., Venkatraman V., Devignes M.D, & Ritchie D.W. (2010). HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 38(Web Server issue), W445-W449.
Publication 2010
Binding Sites Conferences Electrostatics Epistropheus Ligands Mental Orientation Protein Domain Proteins Rumex Staphylococcal Protein A Visually Impaired Persons
4
CABS-Dock: Peptide Docking Protocol
The CABS-dock docking protocol was developed and validated during the following simulation studies: mechanism of folding and binding of an intrinsically disordered peptide (5 ), docking antigen-mimicking peptides to an antibody (6 (link)) and docking peptide co-activators to nuclear receptors (7 (link),8 (link)). These studies showed that the method is able to predict complex arrangements close to the native structure. Importantly, in all the validation tests mentioned above, peptides were allowed to be fully flexible and no information about the binding site or peptide conformation was used.
The CABS-dock protocol is a multiscale modeling procedure based on the coarse-grained CABS protein model. The CABS model has been designed to provide significant efficiency in the treatment of protein conformational changes, while preserving high local accuracy (enabling seamless reconstruction to all-atom representation). In the CABS model, each amino acid is represented by up to four interaction centers, simulation dynamics is controlled by the Monte Carlo scheme and the force field is based on statistical potentials (force field is summarized in the Supplementary Data, details have been described elsewhere (9 (link))). Additionally to the aforementioned protein docking studies, we have demonstrated that the CABS protein model enables reliable simulations of protein dynamics: long-term folding mechanisms (10 (link),11 (link)) and short-term fluctuations close to the native state (12 (link),13 (link)). CABS has also been successfully used in protein structure prediction exercises, showing exceptional performance especially in blind predictions of short globular proteins (14 (link)) and large protein fragments (15 (link),16 (link)). Altogether, these studies demonstrate the validity of the CABS interaction model and sampling scheme in simulations of simultaneous folding and binding, such as performed in the CABS-dock protocol.
Kurcinski M., Jamroz M., Blaszczyk M., Kolinski A, & Kmiecik S. (2015). CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic Acids Research, 43(Web Server issue), W419-W424.
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Publication 2015
Amino Acids Antigens Binding Sites CAB protocol Eye Immunoglobulins Peptide Receptor Peptides Post-Translational Protein Processing Proteins Reconstructive Surgical Procedures Rumex SCAB protocol Staphylococcal Protein A
5
Automated Docking of Diverse Protein Structures
For each target, we assembled all
UniProt accession codes (species) with any raw ChEMBL compounds (ligands,
decoys, marginal ligands, or marginal decoys). For only those accession
codes, structures were extracted using the ChEMBL to PDB mapping,
except P07700 was manually added to ADRB1 to include six more rare
structures for that GPCR. This procedure neglects those PDB structures
that belong to an accession code having no ChEMBL compounds. For example, 1KIM is the PDB structure
of thymidine kinase (KITH) in the original DUD. This KITH structure
is from herpes virus (UniProt P03176), an accession code with no raw
compounds extracted from ChEMBL, and is thus not included in the ChEMBL/PDB
intersection used to construct the new DUD. Still, 5025 PDB codes
were sent to an updated DOCK Blaster pipeline for automated docking
preparation (Supporting Information Figure S1D). In some cases, an unambiguous ligand could not be found to indicate
the binding site, but we were able to assign 565 additional ligands
by manually inspecting over 1300 structures. Ultimately, 3692 structures
completed input grid preparation, and all but two finished docking
and enrichment analysis. Clustered ligands sets were docked to property-matched
decoys (both described below) using ECFP4 fingerprints and removing
the most similar 75% of queried decoys. DOCK 3.6 was run using SEV
ligand desolvation (as below). For each target, enrichment, resolution,
and organism were collected and sorted by enrichment in pdb_analyze.txt,
available online at http://dude.docking.org. Crude notes
on the selection process are recorded in pdb_selection.txt, and the
picked structure is listed in pdb_blessed.txt. AA2AR and DRD3 docking
preparations were provided by Jens Carlson,44 (link),45 CXCR4 partially by Dahlia Weiss,3 (link) ADRB1
by Peter Kolb (personal communication), and AMPC by Sarah Barelier,
Oliv Eidam, and Inbar Fish (unpublished results).
Mysinger M.M., Carchia M., Irwin J.J, & Shoichet B.K. (2012). Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. Journal of Medicinal Chemistry, 55(14), 6582-6594.
Publication 2012
ADRB1 protein, human Binding Sites CXCR4 protein, human Dahlia Fishes Ligands Rumex Simplexvirus Thymidine Kinase

Most recents protocols related to «Rumex»

1
FXR-GW 4064 Complex Structural Insights
The crystal structures of the complex of farnesoid X receptor (FXR) and GW 4064 were downloaded from RCSB Protein Data Bank (PDB ID: 3dct, https://www.rcsb.org/) and prepared by SYBYL-X 2.0. The docking analysis was performed using the Surflex-Dock GeomX (SFXC) in SYBYL-X 2.0. The binding interaction was generated using PyMOL and ligplot.
Tang B., Tang L., Li S., Liu S., He J., Li P., Wang S., Yang M., Zhang L., Lei Y., Tu D., Tang X., Hu H., Ouyang Q., Chen X, & Yang S. (2023). Gut microbiota alters host bile acid metabolism to contribute to intrahepatic cholestasis of pregnancy. Nature Communications, 14, 1305.
Full text: Click here
Publication 2023
GW 4064 Rumex
2
Molecular Target Identification Network
The screened ingredients and the overlapping target genes were utilized to build the active component-target-AR network using Cytoscape 3.7.3 software. In addition, the top six components in the Degree value of THD were selected to dock with key genes.
Zhang F., Wu J., Shen Q., Chen Z, & Qiao Z. (2023). Investigating the mechanism of Tongqiao Huoxue decotion in the treatment of allergic rhinitis based on network pharmacology and molecular docking: A review. Medicine, 102(10), e33190.
Full text: Click here
Publication 2023
Genes Genes, Overlapping Rumex
3
In-silico Validation of BXSM-Target Binding
In order to verify the binding of BXSM compounds to the predicted core targets, we retrieved the 3-dimensional molecular structures of BXSM compounds from the PubChem database and retrieved the structure files of target proteins from the RCSB Protein Data Bank database (http://www.rcsb.org/ [accessed on October 19, 2022]).[27 (link)] Molecular docking computations were conducted by using the CB-Dock web service (accessed on October 19, 2022) (https://cadd.labshare.cn/cb-dock2/php/index.php).[28 (link)]
Zhang Y., Zhang Z., Wang S.J., Yang J.N., Zhao Z.M, & Liu X.J. (2023). Molecular targets and mechanisms involved in the action of Banxia Shumi decoction in insomnia treatment. Medicine, 102(10), e33229.
Publication 2023
Protein Targeting, Cellular Rumex
4
Docking of RPR into hERG1 Structure
Docking of RPR into the recently solved cryo-EM structure of hERG1 (open state, PDB: 5VA1, Wang and Mackinnon, 2017 (link)) was performed using the program Gold 4.0.1 (Cambridge DataCentre, Cambridge, United Kingdom) (Jones et al., 1995 (link)). To introduce protein flexibility, 20 snapshots, derived from previous WT hERG1 all-atom molecular dynamics simulations were used for docking (Zangerl-Plessl et al., 2020 (link)). Coordinates of the geometric center calculated among residues V549, L550, L553, F557, N658, I662, L666 and R681 (Perry et al., 2007 (link); Gardner and Sanguinetti, 2015 (link)) were taken as binding site origin. The side chains of these residues were kept flexible. The binding site radius was set to 15 Å and 150,000 operations of the GOLD genetic algorithm were used to dock the compound.
Zangerl-Plessl E.M., Wu W., Sanguinetti M.C, & Stary-Weinzinger A. (2023). Binding of RPR260243 at the intracellular side of the hERG1 channel pore domain slows closure of the helix bundle crossing gate. Frontiers in Molecular Biosciences, 10, 1137368.
Full text: Click here
Publication 2023
Binding Sites Gold Proteins Radius Reproduction Rumex
5
Computational Screening of Rosmarinic Acid
Initially, (R)-(+)-rosmarinic acid was chosen as a ligand molecule and retrieved from the chemical database to find out its antiviral potential against the proteins of dengue and herpes viruses. Similar to the ligand, the viral proteins were retrieved from the protein database (www.rcsb.com) as in crystallographic form to dock with (R)-(+)-rosmarinic acid. The alphanumeric identities of the proteins were 1F5Q murine gamma herpesvirus cyclin complexed to human cyclin-dependent kinase 2 (Card et al. 2000 (link)), 2J7W dengue virus NS5 RNA-dependent RNA polymerase domain complexed with 3’dGTP (Yap et al. 2007 (link)), and 4OIG dengue virus nonstructural protein NS1 (Edeling et al. 2014 (link)).
Samy C.R., Karunanithi K., Sheshadhri J., Rengarajan M., Srinivasan P, & Cherian P. (2023). (R)-(+)-Rosmarinic Acid as an Inhibitor of Herpes and Dengue Virus Replication: an In Silico Assessment. Revista Brasileira De Farmacognosia, 33(3), 543-550.
Publication 2023
Antiviral Agents CDK2 protein, human Crystallography Cyclins Dengue Fever Dengue Virus deoxyguanosine triphosphate Gamma Rays Herpesviridae Ligands Mus Proteins RNA-Directed RNA Polymerase rosmarinic acid Rumex Simplexvirus Viral Nonstructural Proteins Viral Proteins

Top products related to «Rumex»

1
Tools by AutoDock
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AutoDock Tools is a software suite designed to perform molecular docking simulations. It provides a graphical user interface (GUI) for preparing input files, running docking calculations, and analyzing the results. The core function of AutoDock Tools is to predict the preferred binding orientations and affinities between a small molecule and a target protein.
2
Tools 1 by AutoDock
Sourced in United States
AutoDock Tools 1.5.6 is a molecular docking software package. It allows users to perform automated docking of ligands (small molecules) to protein receptors. The software provides a graphical user interface for preparing input files, running docking calculations, and analyzing the results.
3
Vina 1 by AutoDock
Sourced in United States
AutoDock Vina 1.1.2 is a software application designed for molecular docking. It is capable of predicting the binding affinity and orientation of small molecules (ligands) to a given protein (receptor). The software uses a hybrid global-local search engine and a scoring function to evaluate the potential binding interactions between the ligand and the receptor.
4
Sybyl x 2 by Tripos
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SYBYL-X 2.0 is a molecular modeling software suite developed by Tripos. It provides tools for the visualization, analysis, and manipulation of molecular structures. The software supports a variety of file formats and enables users to perform tasks such as molecular docking, conformational analysis, and pharmacophore modeling.
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Discovery Studio is a comprehensive software platform for molecular modeling, simulation, and analysis. It provides a wide range of tools and functionalities for studying the structural and functional properties of biomolecules, including proteins, small molecules, and nucleic acids. The software enables researchers to visualize, analyze, and manipulate molecular structures, as well as perform various computational experiments and analyses.
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The Gel Dock is a laboratory device used to capture and analyze images of electrophoresis gels. It provides a controlled environment for imaging and documentation of gel-based experiments.
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LigPrep is a software tool designed to prepare chemical structures for computational modeling and analysis. It performs a variety of structure preparation tasks, including generating 3D molecular structures, adding hydrogen atoms, and adjusting ionization states. LigPrep is a useful tool for preparing chemical compounds for further computational studies.
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More about "Rumex"

Rumex, a genus of perennial herbs, are renowned for their edible leaves and roots, often referred to as docks or sorrels.
These plants are widely distributed across temperate regions, characterized by their distinctive leaf shapes ranging from lanceolate to hastate, and their inconspicuous flowers that develop into dry fruits.
Rumex species hold significant medicinal and culinary value, making them a subject of interest for researchers.
To assist scientists in their Rumex research, PubCompare.ai's AI-driven platform offers a seamless solution.
This platform enables researchers to locate the most relevant and reliable protocols from the vast body of literature, including publications, preprints, and patents.
With its typo-tolerant search capabilities, PubCompare.ai ensures that even minor spelling errors do not hinder the discovery of crucial information.
In addition to the MeSH term description, researchers studying Rumex may find the following tools and software useful in their work: - AutoDock Tools and AutoDock Tools 1.5.6: These tools facilitate the preparation of ligands and receptors for molecular docking studies, which can be valuable in understanding the interactions between Rumex compounds and their targets. - AutoDock Vina 1.1.2: This software provides efficient and accurate molecular docking capabilities, enabling researchers to explore the binding affinities and interactions between Rumex compounds and various biomolecules. - SYBYL-X 2.0, Discovery Studio, and Maestro: These molecular modeling and simulation platforms can assist in the structural analysis, conformational studies, and virtual screening of Rumex-related compounds. - Protein Preparation Wizard and LigPrep: These tools can help in the preparation and optimization of protein structures and ligand molecules, which is crucial for downstream computational studies involving Rumex.
By leveraging these advanced tools and software, researchers can enhance the reproducibility and accuracy of their Rumex studies, ultimately leading to a deeper understanding of the properties, interactions, and potential applications of these fascinating plants.