Results 1 to 10 of about 1,526,997 (293)

Method for Computing Protein Binding Affinity [PDF]

Journal of Computational Chemistry, 2004
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move which ...
Adams, Bayly, Bennett, Case, Cornell, Dempster, Frisch, Gilson, Golub, Hamilton, Hawkins, Head, Houdayer, Katz, Kollman, Kong, Landau, Luo, Lyubartsev, Mardia, Mares-Guia, Metropolis, Mezei, Miller, Morris, Schwarzl, Senderowitz, Senderowitz, Still, Tidor, Tsui, Verbeek, Voter, Zhu   +33 more
core   +5 more sources

Methods for Improving Aptamer Binding Affinity [PDF]

Molecules, 2016
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always ...
Hijiri Hasegawa, Nasa Savory, Koichi Abe, Kazunori Ikebukuro   +3 more
doaj   +3 more sources

Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions

iScience, 2023
Summary: CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS).
Ester Marina-Zárate, Ana Rodríguez-Ronchel, Manuel J. Gómez, Fátima Sánchez-Cabo, Almudena R. Ramiro   +4 more
doaj   +4 more sources

Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.

PLoS Computational Biology, 2023
Accurate binding affinity prediction (BAP) is crucial to structure-based drug design. We present PATH+, a novel, generalizable machine learning algorithm for BAP that exploits recent advances in computational topology.
Yuxi Long, Bruce R Donald
doaj   +3 more sources

A Folding-Docking-Affinity framework for protein-ligand binding affinity prediction

Communications Chemistry
Accurate protein-ligand binding affinity prediction is crucial in drug discovery. Existing methods are predominately docking-free, without explicitly considering atom-level interaction between proteins and ligands in scenarios where crystallized protein ...
Ming-Hsiu Wu, Ziqian Xie, Degui Zhi
doaj   +3 more sources

DrugForm-DTA: Towards real-world drug-target binding affinity model [PDF]

Computational and Structural Biotechnology Journal
Drug-target affinity (DTA) prediction is a fundamental challenge in drug discovery. Computational methods for predicting DTA can greatly assist drug design by narrowing the search space and reducing the number of protein-ligand complexes with low ...
Ivan Khokhlov, Anna Tashchilova, Nikolai Bugaev-Makarovskiy, Olga Glushkova, Vladimir Yudin, Anton Keskinov, Sergey Yudin, Dmitry Svetlichnyy, Veronika Skvortsova   +8 more
doaj   +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

Learned features of antibody-antigen binding affinity

Frontiers in Molecular Biosciences, 2023
Defining predictors of antigen-binding affinity of antibodies is valuable for engineering therapeutic antibodies with high binding affinity to their targets.
Nathaniel L. Miller, Nathaniel L. Miller, Thomas Clark, Thomas Clark, Rahul Raman, Rahul Raman, Ram Sasisekharan, Ram Sasisekharan   +7 more
doaj   +1 more source

Probing high affinity sequences of DNA aptamer against VEGF165. [PDF]

PLoS ONE, 2012
Vascular endothelial growth factor (VEGF(165)) is a potent angiogenic mitogen commonly overexpressed in cancerous cells. It contains two main binding domains, the receptor-binding domain (RBD) and the heparin-binding domain (HBD). This study attempted to
Harleen Kaur, Lin-Yue Lanry Yung
doaj   +1 more source

Insilico study of stigmasterol extracted from pluchea indica as antiferility in men [PDF]

, 2023
Docking is a method to predict the strength of the interaction between the receptor and the ligand based on the binding affinity value. The docking carried out in this study is a specific docking with a grid box imitating the bond between AR and ...
Fatmawati, Diani, Nurrohman, Endrik, Nuryady, Moh., Susetyarini, Eko, Zainul, Rahadian   +4 more
core   +1 more source