Publications

Highlights

Computed Protein–Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems

We carefully assembled and curated a set of 11 protein–peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding.

Süleyman Selim Çınaroğlu, Philip C Biggin

J. Chem. Inf. Model. 2023, 63, 19, 6095–6108

The role of loop dynamics in the prediction of ligand–protein binding enthalpy

We evaluated the performance of absolute enthalpy of binding calculations using molecular dynamics simulation for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data.

Süleyman Selim Çınaroğlu, Philip C Biggin

Chem. Sci., 2023, 14, 6792-6805

Evaluating the performance of water models with host–guest force fields in binding enthalpy calculations for cucurbit [7] uril–guest systems

We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril–guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam).

Süleyman Selim Çınaroğlu, Philip C Biggin

J. Phys. Chem. B 2021, 125, 6, 1558–1567

Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets

This study reports an extensive testing of different MM-GBSA scoring schemes on two bromodomain (BRD) datasets. The first set is composed of 24 BRPF1 complexes, and the second one is a nonredundant set constructed from the PDBbind and composed of 28 diverse BRD complexes. A variety of MM-GBSA schemes were analyzed to evaluate the performance of four protocols with different numbers of minimization and MD steps, 10 different force fields and three different water models.

Süleyman Selim Çınaroğlu, Emel Timuçin

Briefings in Bioinformatics, 21(6), 2020, 2112–2125

Comparative assessment of seven docking programs on a nonredundant metalloprotein subset of the PDBbind refined

This study reports comparative assessment of seven docking programs (AutoDock4, AutoDock4Zn, AutoDock Vina, Quick Vina 2, LeDock, PLANTS, and UCSF DOCK6) on a diverse metalloprotein set which was compiled for this study. The refined set of the PDBbind (2017) was screened to gather 710 complexes with metal ion(s) closely located to the ligands (<4 Å).

Süleyman Selim Çınaroğlu, Emel Timuçin

J. Chem. Inf. Model. 2019, 59, 9, 3846–3859

 

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