• CD137 ligand (CD137L) is a type II membrane protein and part of the TNF superfamily. (fishersci.com)
  • GITR Ligand, also known as TNFSF18 and TL6, is an approximately 30 kDa type II transmembrane glycoprotein in the TNF superfamily (1). (genscript.com)
  • The TmMe anion is a tridentate, tripodal ligand topologically similar to the more common Tp ligands, but the two classes of ligands differ in several ways. (wikipedia.org)
  • Phosphines and related P(III) ligands constitute one of the most-used classes of ligands in coordination and organometallic chemistry and have great potential for application in homogeneous catalysis. (mdpi.com)
  • The first described CID systems involve microbe-derived dimerizing ligands, such as rapamycin, that direct protein neo-associations that rewire eukaryotic cell signaling 5 . (nature.com)
  • In the auxin and jasmonic acid systems, ligand recognition is shared between protein-binding partners. (nature.com)
  • Hi everyone, I am attempting to run a blind dock of a ligand (chain X) into a protein complex (chains ABCDEF). (rosettacommons.org)
  • B) Half of your flags are for ligand docking and half are for protein-protein docking. (rosettacommons.org)
  • While the ligand docking application does re-use some of the -docking flags, it's a separate application from protein-protein docking, and doesn't use all of them. (rosettacommons.org)
  • Unless there's indications otherwise, it's best to assume that protein-protein-docking issues/options don't apply to ligand docking (except, of course, for general Rosetta issues). (rosettacommons.org)
  • For protein-ligand docking, the reference you're looking for would probably be Meiler & Baker Proteins. (rosettacommons.org)
  • Theoretical calculation of protein-protein and protein-ligand binding free energies is a grand challenge in computational biology. (utoronto.ca)
  • In this talk we develop an efficient approach (Interaction Entropy) to computing quantitative residue-specific contributions to protein-protein and protein-ligand binding free energies. (utoronto.ca)
  • Studies for an extensive set of realistic protein-protein interaction systems and for specific protein-ligand binding systems showed that by including the entropic contribution, the computed residue-specific binding free energies are in better agreement with the corresponding experimental data. (utoronto.ca)
  • 1. Duan, L.L., X. Liu, and J.Z.H. Zhang, Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy. (utoronto.ca)
  • Computational Alanine Scanning with Interaction Entropy for Protein-Ligand Binding Free Energies, J. Chem. (utoronto.ca)
  • In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. (lu.se)
  • We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
  • This entropy largely stems from the fluctuation of the protein and ligand. (lu.se)
  • Additionally, we compared how MD and grand-canonical Monte Carlo (GCMC) can be used to assess dynamics and thermodynamics of protein-ligand binding for both buried and solvent-exposed binding sites. (lu.se)
  • Dear amber users, I have taken few conformations of a ligand(same ligand)from Protein Data Bank. (vanderbilt.edu)
  • We would like to understand the 'driving forces' of protein-ligand binding, which amounts to understanding the statistical thermodynamics of the binding process at atomic resolution. (lu.se)
  • This is perhaps one reason why protein conformational entropy has not received widespread attention in the field of ligand/drug design, while the often dominant role of solvent entropy is generally taken into account, together with the change in ligand entropy. (lu.se)
  • For these reasons, we are interested in the role of the conformational entropy of the target protein in ligand-binding processes. (lu.se)
  • By comparing NMR-derived order parameters between the free and ligand-bound protein, we estimate the contributions from conformational entropy to the free energy of ligand binding. (lu.se)
  • We combine NMR relaxation experiments with molecular dynamics (MD) simulations to derive a highly detailed picture of how the conformational entropy changes when the protein binds different ligands. (lu.se)
  • A crucial contribution to the ligand -receptor binding affinity is, in addition to their electrostatic and van der Waals interactions, the desolvation of the ligand . (rsc.org)
  • There is a great need for PET and SPECT ligands with high affinity and selectivity for the serotonin uptake site. (erowid.org)
  • Compared with the previously published ligand, FAPI-02, FAPI-04 showed excellent stability in human serum, higher affinity for FAP as opposed to CD26, and slower excretion in vitro. (snmjournals.org)
  • SAN DIEGO--(BUSINESS WIRE)--Nov. 18, 2005--Ligand Pharmaceuticals Incorporated (Pink Sheets: LGND) today announced that the board of directors and management of the company believe that, while ongoing operational actions should translate into improved shareholder value, following their continued review of the company's business, product assets, and current strategic position, it is also now appropriate to initiate an external process to explore strategic alternatives to enhance shareholder value. (biospace.com)
  • Two different models are used to represent the ligand-ligand interactions: the TraPPE-UA force field and a coarse-grain model with purely repulsive interactions. (aiche.org)
  • A study published in the journal Science China Chemistry found that PBA3[InCl6]·H2O exhibits a special "herringbone" stacking mode that enables abundant weak interactions between organic ligands and metal halide units. (phys.org)
  • TNFSF18 / GITR Ligand is important for interactions between activated T-lymphocytes and endothelial cells.Recombinant Human GITR Ligand Fc Chimera produced in HEK293 cells is a polypeptide chain containing 359 amino acids with the C-termimal human IgG1 Fc fragment. (genscript.com)
  • In addition to NMR relaxation methods, we use isothermal titration calorimetry to obtain the thermodynamic fingerprint of ligand binding, including the total (standard) free energy, enthalpy, and entropy of the process. (lu.se)
  • This research concerns a new generation of phosphorus ligands bearing short and branched perfluoroalkyl or perfluoropolyether substituents of the fluorine content and their coordination chemistry as an alternative ligands and metal complexes having a potential application in fluorous biphase system in all common organic solvents. (bl.uk)
  • Their electronic and steric characteristics can easily be tuned by varying the three substituents on the phosphorus atom, thus covering an ample range of properties that span from small strong σ-donating ligands such as PMe 3 to bulky less-basic π-accepting ligands such as tris( o -tolyl)phosphite. (mdpi.com)
  • the development of imaging ligands for visualizing changes in receptors or other brain proteins relevant to substance abuse and co-occurring psychiatric disorders (e.g., anxiety, depression), 4. (nih.gov)
  • Plants sense abscisic acid (ABA) using chemical-induced dimerization (CID) modules, including the receptor PYR1 and HAB1, a phosphatase inhibited by ligand-activated PYR1. (nature.com)
  • Free energy perturbation calculations have shown that the significant decrease of the penalty of desolvation, facilitating the entrance of the ligands into the binding site crevice, compensates for the weaker ligand -receptor interaction. (rsc.org)
  • The perfluoroalkylated phosphine, phosphinite, phosphonite ligands have been reacted with transition metal complexes to form complexes of the type cis and trans-[PtCl₂L₂], and [Cp*RhCl₂L]. (bl.uk)
  • The derivatised phosphonic acid ligands have been reacted with transition metal complexes as dianionic bidentate ligands to form coordination complexes of the type [Pt(O₃PR)(PPh₃)₂] and zirconium phosphonate Zr[O₃PC₆H₄-4-R]₂. (bl.uk)
  • A study into potential fluorous solubility of the synthesised ligands and their metal complexes was also undertaken. (bl.uk)
  • P(III) ligands, in either the monodentate form or a polydentate/hybrid form, have played a crucial role in the stabilization of elusive species and unusual structures within transition complexes, allowing for the isolation and/or detection of agostic complexes, σ-alkane adducts, non-heteroatom-stabilized alkylidenes, and low-coordinate unsaturated species, among others. (mdpi.com)
  • With this Special Issue, we aim to present a collection of research and review articles dedicated to the design and applications of phosphines and related ligands, with special reference to the stabilization of elusive and unusual structural motifs in transition metal complexes. (mdpi.com)
  • The AlaSTAT Microplate Allergen-Specific IgE system is an enzyme-labeled immunometric assay, based on liquid allergen complexes, monoclonal antibodies, and separation by ligand-coated wells. (cdc.gov)
  • Ligand-labeled allergen complexes and a patient sample are pipetted into ligand-coated wells and then incubated for 1 hour. (cdc.gov)
  • Addition of a multivalent anti-ligand creates a bridge between the allergen/IgE complexes and the ligand-coated wells during the second 1-hour incubation. (cdc.gov)
  • In coordination chemistry, a ligand is an ion or molecule (see also: functional group) that binds to a central metal atom to form a coordination complex. (phys.org)
  • HIV preferentially infects and replicates in cells expressing the CD4 molecule, the ligand for viral attachment and subsequent cell entry (1). (cdc.gov)
  • In recent years, progress has been made toward understanding the role of biologically produced organic ligands in controlling the speciation and photochemical redox cycling of iron in ocean surface waters. (bioone.org)
  • Ligands in a complex dictate the reactivity of the central atom, including ligand substitution rates, the reactivity of the ligands themselves, and redox. (phys.org)
  • Furthermore, it is important and challenging to accurately model the large entropic contribution to ligand-binding free energies. (lu.se)
  • RÉSUMÉ L'objectif de l'étude était d'évaler l'importance clinique du ligand de CD40 soluble (sCD40L) chez des patients atteints d'un carcinome hépatocellulaire (CHC) associé au virus de l'hépatite C (VHC). (who.int)
  • 99%) of the dissolved iron in seawater is now known to be associated with strong organic ligands. (bioone.org)
  • The mechanism of superoxide-mediated reduction of Fe(III) in the presence of strong Fe(III) organic ligands is also open to debate. (bioone.org)
  • Katherine Barbeau "Photochemistry of Organic Iron(III) Complexing Ligands in Oceanic Systems," Photochemistry and Photobiology 82(6), 1505-1516, (1 November 2006). (bioone.org)
  • In these membranes, inorganic nanoparticles are coated with a shell of organic ligands that interlock as spacers and provide tensile strength. (nature.com)
  • These polymeric ligand exchange columns utilize a range of counter ions to deliver selectivity required for the analysis of carbohydrates, organic acids, and sugar alcohols. (thermofisher.com)
  • Aqueous citrate-stabilized gold nanoparticles (Au NPs) cannot be directly transferred from water to an immiscible organic solution using short alkane ligands. (confex.com)
  • While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall twofold more effective than all other compounds with a reduction up to 85 and 73% of legionella and multi-species biofilms, respectively. (frontiersin.org)
  • aryl phosphonic acid ligands [R-p-C₆H₄P(O)(OH)₂], where R = OCH₂CH₂C₄F₉ or OCH₂CF₂ (OCF₂CF₂)₂OCF₃, and alkyl phosphinite and phosphonite ligands (Ph)ₓP(OR)₃₋ₓwhere R = CH₂CH₂C₄F₉, CH(CH₂OC₄F₉)₂, or CH₂CF₂(OCF₂CF₂)₂OCF₃ have been synthesised and fully characterised by ¹H, ¹⁹F, ³¹P, and ¹³C NMR spectroscopies, and mass spectrometry. (bl.uk)
  • This approach provides a convenient and practical method to modify the Au NP surfaces with short alkyl ligands easily, rapidly, and efficiently, thus having a great potential in facilitating the fabrication of printed flexible electronics, electrical relays, and coupled electronic/photonic computing devices. (confex.com)
  • New data concerning the structure and photochemical reactivity of strong Fe(III) binding ligands (siderophores) produced by pelagic marine bacteria suggest that direct photolysis via ligand-to-metal charge transfer reactions may be an important mechanism for the production of reduced, biologically available iron (Fe[II]) in surface waters. (bioone.org)
  • Further, there are considerable limitations to many of the currently available imaging ligands, including poor selectivity, high cost, or risks from radiation exposure in the case of pediatric populations. (nih.gov)
  • P-selectin glycoprotein ligand-1 ( PSGL-1 ) is a glycoprotein found on white blood cells and endothelial cells that binds to P-selectin (P stands for platelet ), which is one of a family of selectins that includes E-selectin (endothelial) and L-selectin (leukocyte). (wikidoc.org)
  • 1997). "Isolated P-selectin glycoprotein ligand-1 dynamic adhesion to P- and E-selectin" . (wikidoc.org)
  • Human GITR Ligand consists of a 50 amino acid cytoplasmic domain, a 21 aa transsmembrane segment, and a 128 aa extracellular domain (ECD). (genscript.com)
  • Researchers have discovered an extracellular ligand that counteracts muscle wasting in cachexia. (leibniz-gemeinschaft.de)
  • Researchers from the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) in Jena, Germany, show that the extracellular ligand Wnt7a effectively counteracts muscle wasting through activation of the anabolic AKT/mTOR pathway and thereby reverts the loss of muscle stem cell functionality and muscle mass. (leibniz-gemeinschaft.de)
  • The research group "Stem Cells of Skeletal Muscle" lead by Dr. Julia von Maltzahn at the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) in Jena, Germany, investigated the extracellular ligand Wnt7a and was able to show its positive influence on muscle mass and muscle stem cells in cancer cachexia independently of the tumor cell type causing cachexia. (leibniz-gemeinschaft.de)
  • The extracellular ligand Wnt7a activates the anabolic AKT/mTOR pathway in myofibers and reverts the loss of muscle stem cell functionality. (leibniz-gemeinschaft.de)
  • In addition, the extracellular ligand could be used as a supportive treatment during therapy/surgery. (leibniz-gemeinschaft.de)
  • By fragment screening using x-ray crystallography we identified four ligands revealing ligand-binding sites in conserved interfaces between SARS-CoV-2 nsp10 and nsp14/nsp16. (lu.se)
  • Here we show that octahedral coordination of Fe(III) by two mono-anionic facial tris-carbene ligands can suppress such deactivation dramatically. (lu.se)
  • Ligand-field theory enables the 3 d , 4 s , and 4 p orbitals on the metal to overlap with orbitals on the ligand to form the octahedral covalent bond skeleton that holds this complex together. (purdue.edu)
  • The nature of metal-ligand bonding can range from covalent to ionic. (phys.org)
  • Mark D. Spicer, John Reglinski "Soft Scorpionate Ligands Based on Imidazole-2-thione Donors" European Journal of Inorganic Chemistry 2009, Issue 12, pp 1553-1574. (wikipedia.org)
  • Figure 2: Qualitative surface-enhanced Raman scattering (SERS) measurement showing the asymmetric ligand shell of the membrane. (nature.com)
  • This is of special relevance in membrane proteins because the ligand has to be transferred from the aqueous environment to the transmembrane binding site crevice. (rsc.org)
  • The ligand-field model for an octahedral transition-metal complex such as the Co(NH 3 ) 6 3+ ion assumes that the 3 d , 4 s , and 4 p orbitals on the metal overlap with one orbital on each of the six ligands to form a total of 15 molecular orbitals, as shown in the figue below. (purdue.edu)
  • The resulting complex [Fe(phtmeimb)2]+, where phtmeimb is [phenyl(tris(3-methylimidazol-1-ylidene))borate]-, exhibits strong, visible, room temperature photoluminescence with a 2.0 ns lifetime and 2% quantum yield via spin-allowed transition from a ligand-to-metal charge-transfer (2LMCT) state to the ground state (2GS). (lu.se)
  • Furthermore, we conclude that, although partial functional diversification of Kit ligands has been described in other processes, in erythroid development, both paralogs play a similar role, and their function is evolutionarily conserved. (nih.gov)
  • I'm using ligand docking, following the instructions for Rosetta 3.2.1 (my installed version) at http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/ap... . (rosettacommons.org)
  • The Meiler Lab (Jens Meiler did the original Rosetta Ligand docking) also has some tutorials on Rosetta in general, which includes information on ligand docking (See http://www.meilerlab.org/index.php/jobs/resources ). (rosettacommons.org)
  • research seeking to introduce added complexity into their structure to further their functionality has resulted in a handful of examples of heteroleptic structures, whilst the use of unsymmetrical ligands remains underexplored. (rsc.org)
  • The introduction of steric directing groups was also seen to have a profound effect on the cage structures, suggesting that simple ligand modifications could be used to engineer structural properties. (rsc.org)
  • Currently, despite the fact that the flags I'm using should perturb the ligand by a significant amount, the resulting structures are virtually identical (for all chains) to the starting structure, except all chains have been rotated. (rosettacommons.org)
  • Molecular dynamics simulations elucidate the roles of ligand coverage and mobility in producing and maintaining this asymmetry. (nature.com)
  • To determine the role of each ligand in zebrafish, we performed a series of ex vivo and in vivo gain- and loss-of-function experiments. (nih.gov)
  • To further address the role of kitlga and kitlgb in hematopoietic development in vivo, we performed gain-of-function experiments in zebrafish embryos, showing that both ligands cooperate with erythropoietin (Epo) to promote erythroid cell expansion. (nih.gov)
  • It is my impression that the ligand docking standalone executable is deprecated, and it is mostly done via the scripter now. (rosettacommons.org)
  • Metal and metalloids are bound to ligands in virtually all circumstances, although gaseous "naked" metal ions can be generated in high vacuum. (phys.org)
  • Allergens, in a liquid format, are covalently bound to a soluble polymer/copolymer matrix, which in turn is labeled with a ligand - the same ligand used for coating the reaction wells. (cdc.gov)
  • Various ligands in this family are known, differing in what substituents are on the imidazoles. (wikipedia.org)
  • Our new modules enable ligand-programmable multi-channel CID systems for plant and eukaryotic synthetic biology that can empower new plant-based and microbe-based sensing modalities. (nature.com)
  • Starting with the Escherichia coli lac operon in the 1970s, many synthetic ligand-regulated circuits have been built by rewiring natural systems for new functions 1 . (nature.com)
  • Figure 4: Coarse-grained molecular dynamics simulations showing asymmetry in ligand distribution for single nanoparticles and their self-assembled array residing at the air/water interface. (nature.com)
  • We also ran QM/MM simulations on casein-kinase 2 (CK2), where the ligand and a few surrounding residues were treated at the QM level, and the rest of the system at the MM level. (lu.se)
  • Herein we show that it is possible to design unsymmetrical ligands in which either steric or geometric constraints, or both, can be incorporated into ligand frameworks to ensure exclusive formation of single isomers of three-dimensional Pd 2 L 4 metallo-supramolecular assemblies with high fidelity. (rsc.org)
  • R Ligands: Developing of Predictive Structure-Based Bioactive Conformations and Three-Dimensional Structure-Activity Relationships Models for Future Recognition of Abuse Drugs. (bvsalud.org)
  • Although a small number of unsymmetrical ligands have been shown to serendipitously form well-defined metallo-supramolecular assemblies, a more systematic study could provide generally applicable information to assist in the design of lower symmetry architectures. (rsc.org)
  • The TmR anion simulates the environment provided by three facial thiolate ligands but without the 3- charge of a facial trithiolate. (wikipedia.org)
  • This review highlights recent findings, including both model ligand studies and experimental/observational studies of the natural seawater ligand pool. (bioone.org)
  • A third model, based on molecular orbital theory, was therefore developed that is known as ligand-field theory . (purdue.edu)
  • During recent years, the biotic ligand model (BLM) has been proposed as a tool to evaluate quantitatively the manner in which water chemistry affects the speciation and biological availability of metals in aquatic systems. (researchgate.net)
  • For example, there is currently no ligand available for non-invasive imaging of latent HIV in the human brain, which would be valuable for treatment of HIV/AIDS, or for detection of metabolites and signaling molecules associated with multiple glial cell types, which could shed light on the involvement of glial cell activity in substance use disorders (SUD). (nih.gov)
  • the development of imaging ligands for visualizing neuronal and/or glial retrograde/signaling molecules (e.g., glutamine, anandamide). (nih.gov)
  • The facility is open to all researchers at Lund University, and the prices for production of already established ligands are subsidised for all MulltiPark researchers. (lu.se)
  • In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water ( Aeromonas hydrophila , Pseudomonas aeruginosa , Escherichia coli , Klebsiella pneumoniae ). (frontiersin.org)
  • The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. (phys.org)
  • Furthermore, the metal-ligand bond order can range from one to three. (phys.org)
  • Ligands are classified in many ways: their charge, their size (bulk), the identity of the coordinating atom(s), and the number of electrons donated to the metal (denticity or hapticity). (phys.org)
  • Within the ECD, human GITR Ligand shares 56% and 60% aa sequence identity with mouse and rat GITR Ligand, respectively. (genscript.com)
  • No.: Z03440) at 5.0 μg/ml (100 µl/well) can bind human biotinylated GITR Ligand, hFc, Human when detected by Streptavidin-HRP. (genscript.com)
  • Human ICOS ligand (ICOSLG) ELISA kit is Available at Gentaur Genprice with the fastest delivery. (joplink.net)