Results 21 to 30 of about 1,037,789 (311)

Computational Design of Nanobody Binding to Cortisol to Improve Their Binding Affinity Using Molecular Docking and Molecular Dynamics Simulations

Indonesian Journal of Chemistry, 2022
Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity.
Umi Baroroh, Nur Asni Setiani, Irma Mardiah, Dewi Astriany, Muhammad Yusuf   +4 more
doaj   +1 more source

Cyclopentadienyltricarbonylrheniumbenzazepines: synthesis and binding affinity

Bioorganic & Medicinal Chemistry Letters, 2000
Analogues of the benzazepine dopamine D1 receptor antagonist SCH-23390 incorporating the cyclo-pentadienyltricarbonyl-rhenium (CPTR) moiety were synthesized and evaluated pharmacologically. The CPTR derivatives retained affinity (0.3-2.9 nM) and D1 selectivity of the parent compound, supporting their use as neuropharmacological surrogates for 99mTc ...
G, Tamagnan, R M, Baldwin, N S, Kula, R J, Baldessarini, R B, Innis   +4 more
openaire   +2 more sources

Binding Affinity via Docking: Fact and Fiction

Molecules, 2018
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known ...
Tatu Pantsar, Antti Poso
doaj   +1 more source

Cyanovirin-N Binds Viral Envelope Proteins at the Low-Affinity Carbohydrate Binding Site without Direct Virus Neutralization Ability

Molecules, 2021
Glycan-targeting antibodies and pseudo-antibodies have been extensively studied for their stoichiometry, avidity, and their interactions with the rapidly modifying glycan shield of influenza A. Broadly neutralizing antiviral agents bind in the same order
Irene Maier, Robert H. Schiestl, Georg Kontaxis   +2 more
doaj   +1 more source

Structure and affinity of DNA binding peptides [PDF]

Nucleic Acids Symposium Series, 2000
Artificial peptides designed to form alpha-helical, beta-turn, antiparallel beta-sheet and beta-hairpin structures which are among the motifs most frequently found in natural DNA/RNA binding proteins were synthesized and their characteristic features were examined in the presence or absence of double or triple stranded DNA by means of UV melting ...
T, Kubo, K, Yokoyama, R, Ueki, S, Abe, K, Goto, T, Niidome, H, Aoyagi, K, Iwakuma, S, Ando, S, Ono, M, Fujii   +10 more
openaire   +2 more sources

FoldAffinity: binding affinities from nDSF experiments [PDF]

Scientific Reports, 2021
AbstractDifferential scanning fluorimetry (DSF) using the inherent fluorescence of proteins (nDSF) is a popular technique to evaluate thermal protein stability in different conditions (e.g. buffer, pH). In many cases, ligand binding increases thermal stability of a protein and often this can be detected as a clear shift in nDSF experiments.
Niebling, Stephan, Burastero, Osvaldo, Bürgi, Jérôme, Günther, Christian, Defelipe, Lucas Alfredo, Sander, Simon, Gattkowski, Ellen, Anjanappa, Raghavendra, Wilmanns, Matthias, Springer, Sebastian, Tidow, Henning, García Alai, María   +11 more
openaire   +4 more sources

A Beginner’s Guide to Molecular Docking

Sciences of Phytochemistry, 2022
In this opinion, the basics of molecular docking (MD) such as binding affinity, binding pose, and ligand interactions with common docking-related terminologies (Apo protein, positive control, native ligand, co-crystal inhibitors) are discussed.
James H. Zothantluanga, Dipak Chetia
doaj   +1 more source

Inhibition of sequestration of human B-2 bradykinin receptor by phenylarsine oxide or sucrose allows determination of a receptor affinity shift and ligand dissociation in intact cells [PDF]

, 2004
Depending on their interaction with intracellular proteins, G proteincoupled receptors (GPCR) often display different affinities for agonists at 37degreesC. Determining the affinity at that temperature is often difficult in intact cells as most GPCRs are
Faussner, Alexander, Jochum, Marianne, Schuessler, Steffen, Seidl, Cornelia   +3 more
core   +1 more source

PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees

Frontiers in Genetics, 2019
Protein-RNA interactions play essential roles in many biological aspects. Quantifying the binding affinity of protein-RNA complexes is helpful to the understanding of protein-RNA recognition mechanisms and identification of strong binding partners.
Lei Deng, Lei Deng, Wenyi Yang, Hui Liu
doaj   +1 more source

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity

Journal of Cheminformatics, 2023
Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding affinity and thus impact the drug’s efficacy and side effects.
Ammar Ammar, Rachel Cavill, Chris Evelo, Egon Willighagen   +3 more
doaj   +1 more source