Results 41 to 50 of about 107,002 (300)

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach. [PDF]

, 2017
Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations.
Abagyan, Ruben, Lam, Polo C-H, Totrov, Maxim   +2 more
core   +2 more sources

Computational insights into the inhibitory mechanism of human AKT1 by an orally active inhibitor, MK-2206.

PLoS ONE, 2014
The AKT signaling pathway has been identified as an important target for cancer therapy. Among small-molecule inhibitors of AKT that have shown tremendous potential in inhibiting cancer, MK-2206 is a highly potent, selective and orally active allosteric ...
Mohd Rehan, Mohd A Beg, Shadma Parveen, Ghazi A Damanhouri, Galila F Zaher   +4 more
doaj   +1 more source

Peptides binding cocaine: A strategy to design biomimetic receptors [PDF]

, 2013
A computational methodology for designing and rationalizing the selection of small peptides as biomimetic receptors for cocaine is proposed. The method started by searching and filtering proteins X-ray and NMR data of biological receptor-cocaine ...
Compagnone, Dario, Curini, Roberta, Del Carlo, Michele, Mascini, Marcello, Montero-Cabrera, Luis Alberto, Perez, German, Sergi, Manuel   +6 more
core   +1 more source

Investigating the potential therapeutic compounds of Equisetum ramosissimum Desf. against uropathogenic Escherichia coli through molecular docking, MD simulation, ADMET and toxicity predictions

In Silico Research in Biomedicine
Introduction: Urinary tract infections (UTIs) are one of the most serious public health problems and preventive through plant-based products with the lead from traditional herbal practices. Methods: The present study aimed to screen the drug potential of
Jeyalatchagan Sureshkumar, Singamoorthy Amalraj, Govidaraju Varatharaju, Srinivasan Prabhu, Muniappan Ayyanar   +4 more
doaj   +1 more source

Structural insights into an engineered feruloyl esterase with improved MHET degrading properties

FEBS Letters, EarlyView.
A feruloyl esterase was engineered to mimic key features of MHETase, enhancing the degradation of PET oligomers. Structural and computational analysis reveal how a point mutation stabilizes the active site and reshapes the binding cleft, expading substrate scope.
Panagiota Karampa, Konstantinos Makryniotis, Theofani‐Iosifina Sousani, Evangelos Topakas, Vangelis Daskalakis, Maria Dimarogona   +5 more
wiley   +1 more source

Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors

, 2019
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force (BPMF) - the binding free energy between a flexible ligand and a rigid receptor - for a small organic ligand and a biological macromolecule ...
Minh, David D. L
core   +1 more source

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

On the Integration of Pharmacophore Model and Molecular Docking Method

Journal of Algorithms & Computational Technology, 2011
Structure-based molecular docking has been recognized as the most effective virtual screening technology. Two aspects decide the accuracy of virtual screening result: one is the simulation degree to the interaction of ligands and acceptors, the other is ...
G. Dong, X.J. Deng, J.H. Xiao
doaj   +1 more source

Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study

Biology, 2023
CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native ...
Prasanna J. Patil, Subodh A. Kamble, Maruti J. Dhanavade, Xin Liang, Chengnan Zhang, Xiuting Li   +5 more
doaj   +1 more source

Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation

BioMed Research International, 2022
Cyclooxygenase‐2 (COX‐2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX‐2 inhibitors could lead to new
Sangavi Pandi, Langeswaran Kulanthaivel, Gowtham Kumar Subbaraj, Sangeetha Rajaram, Senthilkumar Subramanian   +4 more
openaire   +2 more sources