ligand-binding sites
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
... Background: Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug ...of ligand binding sites ...
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PocketPicker: analysis of ligand binding-sites with shape descriptors
... actual ligand binding-site usually coincides with the largest pocket of a protein's surface ...the ligand binding-site as the biggest pocket in 83% of the cases on a test set of 67 ...
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A web server for analysis, comparison and prediction of protein ligand binding sites
... Response: Ideally one should compare newly developed prediction method with existing methods as suggested by a reviewer. In past our group also developed a number of methods for predicting ligand interacting ...
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Human neutrophils increase expression of C3bi as well as C3b receptors upon activation
... Although the monoclonal antibody we used to quantitate CR1 and the M 1/70 antibody to CR3 block the ligand binding sites of these receptors, several lines of evidence suggest that the ve[r] ...
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Shortest Geometric Paths Analysis in Structural Biology
... macromolecules has a rich history but analyzing the distances from this surface to other surfaces or volumes has not been extensively explored. Many important questions can be answered quantitatively through these ...
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In Silico Identification of Potential Inhibitors of Dengue Mosquito, Aedes Aegypti Chorion Peroxidase
... Abstract: The three dimensional structure of Aedes aegypti chorion peroxidase was computed by homology modeling. The ModWeb server provided the most accurate model with QMEAN score of 0.642. The protein model consists of ...
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Searching the protein structure database for ligand binding site similarities using CPASS v 2
... determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure ...of ligand-binding sites and permits pair-wise, one versus ...
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AN IN SILICO EXPLORATION FOR NOVEL INHIBITORS OF α-AMYLASE AND α-GLUCOSIDASE EXTRACTED FROM TINOSPORA CORDIFOLIA
... Present study reports the potential of α-amylase and α-glucosidase inhibitory activities of phytoconstituents of the plant, Tinospora cordifolia using an in silico structure-based molecular docking approach. In silico ...
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A Review on Clustering Techniques and Optimization Algorithms for Molecular Docking and DNA Nanotechnology
... protein binding pockets and their ...Protein-Ligand Binding sites for structure based drug design and virtual ligand ...a ligand binding site to modulate function. ...
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Comparative analysis between the protein mcp 1 and neurotrophins involved in alopecia areata
... 5. Ligand binding site in Neurotrophins protein family PDB ID 1SG1 Three ligand binding sites were found in PDB ID 1DOK of protein MCP-1, out of which 1 was selected for further docking ...
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Albumin mediated transport of rose bengal by perfused rat liver Kinetics of the reaction at the cell surface
... surface sites and their affinity for ...the binding of ligand-free albumin to isolated ...the binding of albumin to the cell surface is the functional equivalent of albumin-mediated ...
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Protein ligand interactions: docking, design and protein conformational change
... bulky ligand that does not bind to OmpA due to steric hindrance from the ...the ligand annealing MD for fucosyl chitobiose with OmpA fixed in region 2) the sugar ring was forced into a boat conformation due ...
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Computational Predictions of G Protein Coupled Receptor Structures and Binding Sites
... The large ectodomain of GLP1R interacts strongly with the C-terminal half of its endogenous polypeptide agonist (in this case GLP1). The N-terminus of the ligand binds to the TM bundle and extracellular loops. ...
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trans Tetraaquabis[1,3 bis(4 pyridyl)propane κN]cobalt(II) biphenyl 4,4′ disulfonate monohydrate
... a ligand with multiple binding sites available to construct coordination polymers with varying dimensionalities, or as a counter ion, forming extensive hydrogen-bonding interaction with the water ...
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Shedding Light On General Anesthesia: Uncovering The Molecular Mechanisms For Propofol And Volatile Anesthetics
... photoaffinity ligand for sevoflurane was validated and applied to uncover the unique mechanism of sevoflurane positive modulation of mammalian Shaker ...photoaffinity ligand was in addition to a previously ...
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A Comparative Study of Binding of Different Drugs on gp120: Insight from Molecular Dynamics Simulation Study
... the binding interaction between gp120 and four experimentally known ligands were evaluated with the help of conformational analysis and the binding free energy calculated over 200 ns dynamics using the ...
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Binding responses associated with self-interacting ligands : studies on the self-association and receptor binding of insulin
... THE BINDING OF AN INDEFINITELY ASSOCIATING LIGAND TO ACCEPTOR: CONSIDERATION OF MONOVALENT LIGAND SPECIES BINDING TO A MULTIVALENT ACCEPTOR 2.1 A REVIEW OF THE BACKGROUND LITERATURE 2.1.[r] ...
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VEGF - A Precis’
... receptor binding face and accounts for 65% of the total surface buried within the dimer and is important for the stability of the receptor binding ...for binding to both KDr and ...for binding ...
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A combined 3D-QSAR and docking studies for the In-silicoprediction of HIV-protease inhibitors
... into ligand-based and structure-based methods. Ligand-based approach is frequently applicable in the absence of experimentally resolved protein crystal structure whereas, structure- based method extract the ...
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Structure prediction, molecular dynamics simulation and docking studies of d-specific dehalogenase from rhizobium sp. Rc1
... The key catalytic residues of proteins that might be responsible for binding to a ligand can be investigated using site-directed mutagenesis. It has been established that detrimental mutations in structural ...
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