Compressed images for affinity prediction-2 (CIFAP-2): an improved machine learning methodology on protein-ligand interactions based on a study on caspase 3 inhibitors

Download

index.pdf

Date

2015-01-01

Author

Erdas, Ozlem
Andac, Cenk. A.
Gurkan-Alp, A. Selen
Alpaslan, Ferda Nur
Buyukbingol, Erdem

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

68
views

0
downloads

The aim of this study is to propose an improved computational methodology, which is called Compressed Images for Affinity Prediction-2 (CIFAP-2) to predict binding affinities of structurally related protein-ligand complexes. CIFAP-2 method is established based on a protein-ligand model from which computational affinity information is obtained by utilizing 2D electrostatic potential images determined for the binding site of protein-ligand complexes. The quality of the prediction of the CIFAP-2 algorithm was tested using partial least squares regression (PLSR) as well as support vector regression (SVR) and adaptive neuro-fuzzy inference system (ANFIS), which are highly promising prediction methods in drug design. CIFAP-2 was applied on a protein-ligand complex system involving Caspase 3 (CASP3) and its 35 inhibitors possessing a common isatin sulfonamide pharmacophore. As a result, PLSR affinity prediction for the CASP3-ligand complexes gave rise to the most consistent information with reported empirical binding affinities (pIC50) of the CASP3 inhibitors.

Subject Keywords

Pharmacology, Drug Discovery, General Medicine

URI

https://hdl.handle.net/11511/40512

Journal

JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

DOI

https://doi.org/10.3109/14756366.2014.976566

Collections

Department of Computer Engineering, Article

Suggestions

OpenMETU
Core

Synthesis of 2-aziridinyl phosphonates by modified Gabriel-Cromwell reaction and their antibacterial activities Doğan, Özdemir; Gözen, Ayşe Gül (Elsevier BV, 2011-06-01) A set of new aziridinyl phosphonates (4a-g) were synthesized by using the Gabriel-Cromwell reaction and its modified version developed in this study and their structures confirmed by HRMS, IR. and NMR spectra. All the compounds were screened for their antibacterial activity. They all showed comparable moderate to good growth inhibitory activity in reference to ampicillin and streptomycin. (C) 2011 Elsevier Masson SAS. All rights reserved.
Synthesis of new derivatives of boehmeriasin A and their biological evaluation in liver cancer Guzelcan, Ece Akhan; Baxendale, Ian R.; Atalay, Rengül; Baumann, Marcus (Elsevier BV, 2019-03-15) Two series of boehmeriasin A analogs have been synthesized in short and high yielding processes providing derivatives differing either in the alkaloid's pentacyclic scaffold or its peripheral substitution pattern. These series have enabled, for the first time, comparative studies into key biological properties revealing a new lead compound with exceptionally high activity against liver cancer cell lines in the picomolar range for both well (Huh7, Hep3B and HepG2) and poorly (Mahlavu, FOCUS and SNU475) diffe...
Adaptive neuro-fuzzy inference system (ANFIS): A new approach to predictive modeling in QSAR applications: A study of neuro-fuzzy modeling of PCP-based NMDA receptor antagonists Buyukbingol, Erdem; Sisman, Arzu; Akyıldız, Murat; Alpaslan, Ferda Nur; Adejare, Adeboye (Elsevier BV, 2007-06-15) This paper proposes a new method, Adaptive Neuro-Fuzzy Inference System (ANFIS) to evaluate physicochemical descriptors of certain chemical compounds for their appropriate biological activities in terms of QSAR models with the aid of artificial neural network (ANN) approach combined with the principle of fuzzy logic. The ANFIS was utilized to predict NMDA (N-methyl-D-Aspartate) receptor binding activities of phencyclidine (PCP) derivatives. A data set of 38 drug-like compounds was coded with 1244 calculated...
Measurement of the t(t)over-bar production cross section using events in the e mu final state in pp collisions at root s=13 TeV Khachatryan, V.; et. al. (2017-03-01) The cross section of top quark-antiquark pair production in proton-proton collisions at root s = 13 TeV is measured by the CMS experiment at the LHC, using data corresponding to an integrated luminosity of 2.2 fb(-1). The measurement is performed by analyzing events in which the final state includes one electron, one muon, and two or more jets, at least one of which is identified as originating from hadronization of a b quark. The measured cross section is 815 +/- 9 (stat) +/- 38 (syst) +/- 19 (lumi) pb, in...
Comparison of Bayesian MAP Estimation and Kalman Filter Methods in the Solution of Spatio-Temporal Inverse ECG Problem Aydin, Umit; Serinağaoğlu Doğrusöz, Yeşim (2009-09-12) In this study, spatial only, and spatio-temporal Bayesian Maximum a Posteriori (MAP) methods and an another spatio-temporal method, the Kalman filter approach, are used to solve the inverse electrocardiography (ECG) problem. Training sets are used to obtain the required a priori information for all methods. Two different approaches are employed to calculate the state transition matrix (STM), which maps the epicardial potentials in two consecutive time instants in the Kalman filter method. The first one uses...

Citation Formats

O. Erdas, C. A. Andac, A. S. Gurkan-Alp, F. N. Alpaslan, and E. Buyukbingol, “Compressed images for affinity prediction-2 (CIFAP-2): an improved machine learning methodology on protein-ligand interactions based on a study on caspase 3 inhibitors,” JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, pp. 809–815, 2015, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/40512.