Results 211 to 220 of about 4,190,416 (396)

LysM domains of Medicago truncatula NFP protein involved in Nod factor perception. Glycosylation state, molecular modeling and docking of chitooligosaccharides and Nod factors [PDF]

, 2006
Lonneke Mulder, Benoît Lefebvre, Julie V. Cullimore, Anne Imberty   +3 more
openalex   +1 more source

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands

Journal of Cheminformatics
Protein-ligand docking is a computational method routinely used in many structural biology applications. It usually involves one receptor and one ligand.
Radek Halfar, Jiří Damborský, Sérgio M. Marques, Jan Martinovič   +3 more
doaj   +1 more source

Density of States and Binding Energy Informatics for Exploring Early Disease Detection in MOF‐Metal Oxide Chemiresistive Sensors

Advanced Theory and Simulations, Volume 8, Issue 5, May 2025.
Binding energy and electronic structure calculations are used to assess the ability of metal–organic framework (MOF)‐TiO2 composite materials to detect volatile organic compounds found in human breath. Electronic structure changes are measured by comparing density of states profiles using Wasserstein distances.
Maryam Nurhuda, Ken‐ichi Otake, Susumu Kitagawa, Daniel M. Packwood   +3 more
wiley   +1 more source

Let’s Dock: A Smart Platform for Molecular Docking

Pakistan Journal of Zoology, 2022
Yaruq Jabeen, Nida Ansari, Haroon Rasheed, Muhammad Asif Rasheed, Muhammad Awais, Muhammad Ibrahim, Sumaira Kanwal, Aqsa Khalid, Manzoor Ahmad Zahid, Farrukh Jamil   +9 more
openaire   +1 more source

Molecular Docking Challenges and Limitations

, 2016
Today, the development of new drugs is a challenging task of science. Researchers already applied molecular docking in the drug design field to simulate ligand- receptor interactions. Docking is a term used for computational schemes that attempt to find the “best” matching between two molecules in a complex formed from constituent molecules.
Jahan B. Ghasemi, Azizeh Abdolmaleki, Fereshteh Shiri   +2 more
openaire   +1 more source

Insights into the Dynamics and Binding Mechanisms of the Alkhumra Virus NS2B/NS3 Protease: A Molecular Dynamics Study

Advanced Theory and Simulations, EarlyView.
The ΔRMSF$\Delta {\rm RMSF}$ analysis reveals significant flexibility differences between free NS3 and the NS2B/NS3 complex, with notable deviations in specific regions. Key residues driving NS2B binding are identified, and the protonation state of catalytic serine affects oxyanion hole formation.
Jurica Novak, Shivananda Kandagalla, Ramesh Sistla   +2 more
wiley   +1 more source

Uncertainty quantification of receptor ligand binding sites prediction [PDF]

arXiv
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These oversights can lead to inaccuracies in identifying viable docking sites due to the complexity of high-dimensional ...
arxiv  

PJA2 Suppresses Colorectal Cancer Progression by Controlling HDAC2 Degradation and Stability

Advanced Science, Volume 12, Issue 13, April 3, 2025.
PJA2, an E3 ubiquitin‐protein ligase, actively restrains colorectal cancer (CRC) progression. It targets histone deacetylase 2 (HDAC2) for degradation, which in turn activates the interferon‐induced protein with tetratricopeptide repeats (IFIT) family, effectively hindering tumor growth and promoting apoptosis.
Zhihao Chen, Chaofan Peng, Chi Jin, Ye Wang, Tuo Wang, Peng Yang, Wen Peng, Qingyang Sun, Hengjie Xu, Hongxu Nie, Xiaowei Wang, Junwei Tang, Yueming Sun, Yifei Feng   +13 more
wiley   +1 more source

Molecular docking and analysis of interactions between vascular endothelial growth factor (VEGF) and SPARC protein [PDF]

, 2007
V. Chandrasekaran, Jayakrishna Ambati, Balamurali K. Ambati, Ethan Will Taylor   +3 more
openalex   +1 more source

Excessive MYC Orchestrates Macrophages induced Chromatin Remodeling to Sustain Micropapillary‐Patterned Malignancy in Lung Adenocarcinoma

Advanced Science, Volume 12, Issue 12, March 27, 2025.
Song et al. integrates an evaluating system to characterize malignancy of micropapillary (MP)‐pattern lung adenocarcinoma in vivo or in vitro. They have discovered that intrinsic MYC redundancy expression combined with extrinsic M2‐like macrophage jointly mediate MP‐pattern malignancy.
Xuming Song, Zehao Pan, Yi Zhang, Wenmin Yang, Te Zhang, Hui Wang, Yuzhong Chen, Xinnian Yu, Hanlin Ding, Rutao Li, Pengfei Ge, Lin Xu, Gaochao Dong, Feng Jiang   +13 more
wiley   +1 more source