NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

Gaudreault, Francis; Morency, Louis–Philippe; Najmanovich, Rafaël

doi:10.1093/bioinformatics/btv458

Cited by 66 publications

(51 citation statements)

References 17 publications

(17 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The testosterone molecule and parameters were obtained on the Automated Topology Builder repository (Molecule ID 9924) 44 . The testosterone molecule was docked in the binding site of STARD6 using FlexAID 45 as described in Letourneau et al . 46 .…”

Section: Methodsmentioning

confidence: 99%

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

Létourneau

Bédard

Cabana

et al. 2016

Sci Rep

View full text Add to dashboard Cite

START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

show abstract

Section: Methodsmentioning

confidence: 99%

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

Létourneau

Bédard

Cabana

et al. 2016

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Molecular docking was performed by a PyMOL plug-in—NRGsuite [ 22 ]—under the PyMOL version 1.8 environment. This included the detection of surface cavities in protein and was used as a target binding site for docking simulations.…”

Section: Methodsmentioning

confidence: 99%

The Inhibitory Effect of Extra Virgin Olive Oil and Its Active Compound Oleocanthal on Prostaglandin-Induced Uterine Hypercontraction and Pain—Ex Vivo and In Vivo Study

et al. 2020

View full text Add to dashboard Cite

Primary dysmenorrhea is a common occurrence in adolescent women and is a type of chronic inflammation. Dysmenorrhea is due to an increase in oxidative stress, which increases cyclooxygenase-2 (COX-2) expression, increases the concentration of prostaglandin F2α (PGF2α), and increases the calcium concentration in uterine smooth muscle, causing excessive uterine contractions and pain. The polyphenolic compound oleocanthal (OC) in extra virgin olive oil (EVOO) has been shown to have an anti-inflammatory and antioxidant effect. This study aimed to investigate the inhibitory effect of extra virgin olive oil and its active ingredient oleocanthal (OC) on prostaglandin-induced uterine hyper-contraction, its antioxidant ability, and related mechanisms. We used force-displacement transducers to calculate uterine contraction in an ex vivo study. To analyze the analgesic effect, in an in vivo study, we used an acetic acid/oxytocin-induced mice writhing model and determined uterus contraction-related signaling protein expression. The active compound OC inhibited calcium/PGF2α-induced uterine hyper-contraction. In the acetic acid and oxytocin-induced mice writhing model, the intervention of the EVOO acetonitrile layer extraction inhibited pain by inhibiting oxidative stress and the phosphorylation of the protein kinase C (PKC)/extracellular signal-regulated kinases (ERK)/ myosin light chain (MLC) signaling pathway. These findings supported the idea that EVOO and its active ingredient, OC, can effectively decrease oxidative stress and PGF2α-induced uterine hyper-contraction, representing a further treatment for dysmenorrhea.

show abstract

“…A cut-off radius can be used to restrict the binding site dimensions depending on the ligand. The use of the additional tool GetCleft [108] allows for the inclusion of predicted cavities. KRIPO fingerprint databases can be individually created by users for their own data sets.…”

Section: Binding Site Comparisonmentioning

confidence: 99%

A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

2018

View full text Add to dashboard Cite

The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting. Moreover, the broad variety of binding site modeling approaches, comparison algorithms, and scoring metrics impedes this choice. Herein, we aim to elucidate strengths and weaknesses of binding site comparison methodologies. A detailed benchmark study is the only possibility to rationalize the selection of appropriate tools for different scenarios. Specific evaluation data sets were developed to shed light on multiple aspects of binding site comparison. An assembly of all applied benchmark sets (ProSPECCTs–Protein Site Pairs for the Evaluation of Cavity Comparison Tools) is made available for the evaluation and optimization of further and still emerging methods. The results indicate the importance of such analyses to facilitate the choice of a methodology that complies with the requirements of a specific scientific challenge.

show abstract

NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID

Cited by 66 publications

References 17 publications

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

The Inhibitory Effect of Extra Virgin Olive Oil and Its Active Compound Oleocanthal on Prostaglandin-Induced Uterine Hypercontraction and Pain—Ex Vivo and In Vivo Study

A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

Contact Info

Product

Resources

About