Results 31 to 40 of about 2,570,021 (252)

Prediction of protein-ligand binding affinity with deep learning

Computational and Structural Biotechnology Journal, 2023
The prediction of binding affinities between target proteins and small molecule drugs is essential for speeding up the drug research and design process. To attain precise and effective affinity prediction, computer-aided methods are employed in the drug ...
Yuxiao Wang, Qihong Jiao, Jingxuan Wang, Xiaojun Cai, Wei Zhao, Xuefeng Cui   +5 more
doaj   +1 more source

Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity [PDF]

, 2011
The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks.
Rajendra, Eason, Skylaris Chris-Kriton, Cole, Daniel J., Venkitaraman Ashok R., Hardwick, Bryn, Payne, Mike C., Mike C. Payne, McKenzie, Grahame J., Grahame J. McKenzie, Cole Daniel J., Mike C Payne, Hardwick Bryn, McKenzie Grahame J., Bryn Hardwick, Grahame J McKenzie, Ashok R Venkitaraman, Chris-Kriton Skylaris, Daniel J Cole, Ashok R. Venkitaraman, Eeson Rajendra, Roberts-Thomson Meredith, Skylaris, Chris-Kriton, Payne Mike C., Kowalczykowski, Stephen Charles, Venkitaraman, Ashok R., Rajendra Eeson, Roberts-Thomson, Meredith, Daniel J. Cole, Meredith Roberts-Thomson   +28 more
core   +3 more sources

PBCNet：Computing Relative Binding Affinity of Ligands to a Receptor Based on a Pairwise Binding Comparison Network for Lead Optimization [PDF]

, 2023
Structure-based lead optimization is an open challenge in drug discovery, which is still largely driven by hypotheses and depends on the experience of medicinal chemists.
Geng, Chen, Duanhua, Cao, Xiaomin, Luo, Hualiang, Jiang, Xiaohong, Liu, Dingyan, Wang, Jie, Yu, Zhaojun, Li, Xutong, Li, Jie, Hu, Gang, Wang, Mingyue, Zheng, Xiangtai, Kong, Yanbei, Li   +13 more
core   +2 more sources

Dynamics and thermodynamics of protein-ligand interactions [PDF]

, 2012
Complex networks of protein-ligand interactions underpin cellular function and communication. Disease can arise from disruption of these networks through the alteration of protein-ligand interaction affinities, for example by protein mutation or ligand ...
Malham, Richard William
core   +6 more sources

Reversible domain closure modulates GlnBP ligand binding affinity

PLoS ONE, 2022
Glutamine binding protein (GlnBP) is an Escherichia Coli periplasmic binding protein, which binds and carries glutamine to the inner membrane ATP-binding cassette (ABC) transporter. GlnBP binds the ligand with affinity around 0.1μM measured by isothermal
Qun Chen, Fang Li, Xiaobing Zuo, Jin Chen, Peiwu Qin, Chuhui Wang, Jin Xu, Danyu Yang, Baogang Xing, Ying Liu, Peng Jia, Linling Li, Chengming Yang, Dongmei Yu   +13 more
doaj   +2 more sources

Learning protein binding affinity using privileged information

BMC Bioinformatics, 2018
Background Determining protein-protein interactions and their binding affinity are important in understanding cellular biological processes, discovery and design of novel therapeutics, protein engineering, and mutagenesis studies.
Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas   +3 more
doaj   +1 more source

Specific integrin alpha and beta chain phosphorylations regulate LFA-1 activation through affinity-dependent and -independent mechanisms [PDF]

, 2005
Integrins are adhesion receptors that are crucial to the functions of multicellular organisms. Integrin-mediated adhesion is a complex process that involves both affinity regulation and cytoskeletal coupling, but the molecular mechanisms behind this ...
Susanna C. Fagerholm, Fagerholm, Susanna C., Nurmi, SM, Hilden, Tiina J., Gahmberg, CG, Gahmberg, Carl G., Carl G. Gahmberg, Susanna M. Nurmi, Nurmi, Susanna M., Fagerholm, SC, Tiina J. Hilden, Hilden, TJ   +11 more
core   +1 more source

High-throughput binding affinity calculations at extreme scales

BMC Bioinformatics, 2018
Background Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or ...
Jumana Dakka, Matteo Turilli, David W. Wright, Stefan J. Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V. Coveney, Shantenu Jha   +7 more
doaj   +1 more source

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches [PDF]

, 2012
Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms.
Levisson, M., Smidt, H., Ruigrok, V.J.B., Mark Levisson, Dijkstra, B.W., Hekelaar, J., Dijkstra, Bauke W., Hauke Smidt, Ruigrok, Vincent J.B.,, van der Oost, John, Bauke W. Dijkstra, Smidt, Hauke,, Hekelaar, Johan, Dijkstra, Bauke W.,, Hekelaar, Johan,, Vincent J. B. Ruigrok, Levisson, Mark,, Oost, J., van der, Levisson, Mark, Smidt, Hauke, Johan Hekelaar, John Van der Oost, van der Oost, J., Oost, John van der,, Ruigrok, Vincent J. B.   +24 more
core   +3 more sources

Affinity-enhanced RNA-binding domains as tools to understand RNA recognition

, 2023
Understanding how the RNA-binding domains of a protein regulator are used to recognize its RNA targets is a key problem in RNA biology, but RNA-binding domains with very low affinity do not perform well in the methods currently available to characterize ...
Evangelos Christodoulou (30025), Giancarlo Abis (7851488), Ian A Taylor (8117153), Belén Chaves-Arquero (11630811), Katherine M Collins (9211667), Geoff Kelly (212365), Andres Ramos (2479399)   +6 more
core   +1 more source