Results 61 to 70 of about 256,731 (319)

A new protein-ligand docking software with an improved method of molecular conformation optimization

, 2023
We study methods of non-linear global optimization in the problem of molecular docking and present a new implementation of protein-ligand docking and preparation of molecules for docking in a new open source software Hess.
Rafael, Temirgaliev, Dmitry, Pavlov
core   +1 more source

Interpreting the effects of DNA polymerase variants at the structural level

Molecular Oncology, EarlyView.
Using MAVISp and molecular dynamics simulations, we analyzed over 60 000 missense variants in POLE and POLD1 from ClinVar, COSMIC, cBioPortal, and saturation mutagenesis. Identified mechanistic indicators, including stability, binding, and long‐range, enable structural interpretation, providing ACMG‐like evidence for possible reclassification of VUS ...
Matteo Arnaudi, Karolina Krzesińska, Ludovica Beltrame, Pablo Sánchez‐Izquierdo Besora, Matteo Tiberti, Mef Nilbert, Anna Rohlin, Elena Papaleo   +7 more
wiley   +1 more source

Docking-Based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase-2

, 2016
The cell division cycle is controlled by cyclin-dependent kinases (cdk), which consist of a catalytic subunit (cdk1-cdk8) and a regulatory subunit (cyclin A−H).
Jaroslav Koča (1355511), Michal Otyepka (64526), Věra Siglerová (3024354), Libor Havlíček (3024357), Vladimír Kryštof (2521318), Miroslav Strnad (157788)   +5 more
core   +1 more source

Binding hotspots of BAZ2B bromodomain:histone interaction revealed by solution NMR driven docking [PDF]

, 2014
Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective targeting of the BAZ2B bromodomain by small molecule inhibitors has been recently reported, but no ...
Ferguson, Fleur M., Alexandre M. J. J. Bonvin (18079), Alexandre M. J. J. Bonvin, João P. G. L. M. Rodrigues (1312506), Wienk, Hans, Fleur M. Ferguson (1304613), Rolf Boelens (18078), Alessio Ciulli, Boelens, Rolf, NMR Spectroscopy, Chris Abell, Fleur M. Ferguson, Garcia Lopes Maia Rodrigues, João, Rodrigues, João P. G. L. M., David M. Dias, Bonvin, Alexandre M. J. J., Sub NMR Spectroscopy, Dias, David M., João P. G. L. M. Rodrigues, David M. Dias (1340694), Rolf Boelens, Abell, Chris, Hans Wienk (684663), Ciulli, Alessio, Hans Wienk, Chris Abell (197099), Alessio Ciulli (762789)   +26 more
core   +1 more source

A novel quinazolinone insulin receptor inhibitor and its synergy with an EGFR inhibitor in glucose‐driven glioblastoma

Molecular Oncology, EarlyView.
The novel styrylquinazolinone‐based molecule W1B effectively suppresses glioblastoma by inhibiting IGF1R and EGFR. In high‐glucose microenvironments driving tumor resistance, W1B acts synergistically with the EGFR inhibitor dacomitinib. This combination safely blocks compensatory survival signaling in zebrafish xenograft models. Showcasing promising in
Patryk Rurka, Wioleta Cieślik, Wojciech Płaziński, Katarzyna Stępnik, Anna Boguszewska‐Czubara, Elżbieta Kot, Robert Musioł, Mateusz Jasica, Anna Mrozek‐Wilczkiewicz, Katarzyna Malarz   +9 more
wiley   +1 more source

Molecular Docking Study of Novel COVID-19 Protease with Low Risk Terpenoides Compounds of Plants

, 2020
Background :Due to the reported high ability of virulence of COVID_19 in recent months, several studies have been conducted to discover and introduce COVID_19 antiviral drugs.
Neda, Shaghaghi
core   +1 more source

Synergistic Application of Molecular Docking and Machine Learning for Improved Protein-Ligand Binding Pose Prediction

, 2023
Accurate prediction of protein-ligand complex structures is a crucial step in structure-based drug design. Traditional molecular docking methods exhibit limitations in terms of accuracy and sampling space, while relying on machine-learning approaches may
Yannan, Yuan, Hang, Zheng, Yaqi, Li, Hongrui, Lin, Rongfeng, Zou, Linfeng, Zhang, Gengmo, Zhou, He, Yang   +7 more
core   +1 more source

Study on Improvement of Docking Mechanism for Docking–Undocking Drones in the Air and Docking Control Using an Onboard Camera

Journal of Robotics and Mechatronics
In this study, we developed a docking mechanism for drones that enables docking and undocking in the air for cargo transportation. This capability allows the drone configuration to be adapted depending on the cargo size and shape. We introduced a novel docking mechanism that incorporates magnetic adsorption and a newly engineered locking mechanism.
Rikiya Dohi, Yoshiyuki Higashi
openaire   +1 more source

Validation Studies of the Site-Directed Docking Program LibDock [PDF]

Journal of Chemical Information and Modeling, 2007
The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I.
Shashidhar N. Rao, Martha S. Head, Amit Kulkarni, Judith M. LaLonde   +3 more
openaire   +2 more sources

In vitro and in silico modelling of ROS1‐positive non‐small cell lung cancer reveals fusion‐dependent tyrosine kinase inhibitor responses

Molecular Oncology, EarlyView.
Drug resistance limits treatment success in a subset of lung cancers driven by ROS1 gene alterations. Using patient‐derived cells and computer simulations, we studied three key mutations and how they affect five targeted drugs. The mutations reduced drug effectiveness in different ways by altering protein structure and behavior.
Farhan Ul Haq, Marc Terrones, Felicia Rodrigues Fortes, Anne Schepers, Alessia Denis, Christophe Deben, Ken Op de Beeck, Guy Van Camp, Geert Vandeweyer   +8 more
wiley   +1 more source