2012
DOI: 10.1590/s0103-50532012005000082 View full text |Buy / Rent full text
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Abstract: Neste estudo, simulações de dinâmica molecular (MD) e docking foram realizadas a fim de investigar o sítio de ligação e as interações de 61 inibidores com o receptor de kinase-5 do tipo ativina (ALK5). Uma simulação MD foi realizada sobre o receptor para obter sua conformação em água. A análise de docking revelou que interações do tipo ligação hidrogênio e hidrofóbicas desempenham papéis importantes no complexo inibidor-ALK5. Estas interações foram confirmadas por cristalografia de raios X. Além disso, para es… Show more

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“…spacing of 0.375Å (Chinnadurai et al, 2015;Ebrahimi et al, 2012;Cohen et al, 2011). This was done in such a way so as to enclose the active site residues where the ligands could rotate around flexibly.…”
Section: Chemicalsmentioning
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“…spacing of 0.375Å (Chinnadurai et al, 2015;Ebrahimi et al, 2012;Cohen et al, 2011). This was done in such a way so as to enclose the active site residues where the ligands could rotate around flexibly.…”
Section: Chemicalsmentioning
“…LASSO shrinks the coefficients of the insignificant variables to zero, and the most effective variables are selected according to the cross‐validation prediction error. Recently, LASSO has been considered in QSAR/QSPR studies as a modeling approach 17–20 . There is only one report on the application of LASSO as variable selection before nonlinear modeling by support vector machine (LASSO‐SVM), in which the performance of LASSO has been compared with random forest (RF) as a variable selection method 21 .…”
Section: Introductionmentioning
“…The results from the established QSAR models help researchers to find a quantitative relationship between structures and biological activities that leads to the design of new compounds with remarkable biological activities with no need for any experimental studies (Muhammad et al 2018;Ojha Lokendra et al 2013). In recent years, the three-dimensional (3D) structures for a wide variety of receptors have become available and also the computational methods have greatly improved; thus, the use of descriptors containing information about the interactions of ligands with the active site of receptors has been highly suggested in the QSAR studies (Amini et al 2016;Chakraborty et al 2014;Chen and Chen 2012;Coi and Bianucci 2013;Davood and Iman 2011;Ebrahimi and Khayamian 2014;Ebrahimi et al 2012;Garg et al 2010;Gharaghani et al 2013;Rasouli and Davood 2018;Safarizadeh and Garkani-Nejad 2019;Sheikhpour et al 2017;Singla et al 2011;Zheng et al 2014). Among the computational chemistry methods, molecular docking is a powerful tool that provides the LR interaction information (Gharaghani et al 2013) through the different computational software such as Dock and AutoDock (Kramer et al 1999;Morris et al 1998).…”
Section: Introductionmentioning
“…The descriptors computed in this way are in fact the same as the structural descriptors; however, because they are calculated from the modified structure of the docked ligand, they have to some extent the interaction information but do not fully reflect the LR interactions. The other way is the extraction of MDDs as the interactions information from the best conformation of LR complex after successful docking of each ligand in the active site of the receptor (Amini et al 2016;Chakraborty et al 2014;Chen and Chen 2012;Coi and Bianucci 2013;Davood and Iman 2011;Ebrahimi and Khayamian 2014;Ebrahimi et al 2012;Garg et al 2010;Gharaghani et al 2013;Rasouli and Davood 2018;Safarizadeh and Garkani-Nejad 2019;Sheikhpour et al 2017;Singla et al 2011;Zheng et al 2014). The MDDs computed in this way are of the LR binding energy and enter the LR interaction information into the QSAR models, successfully.…”
Section: Introductionmentioning
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