An evaluation of combined strategies for improving the performance of molecular docking

S Xu, L Wang, X Pan - Journal of bioinformatics and computational …, 2021 - World Scientific
Molecular docking is a fast and efficient computational method for the prediction of the
binding mode and binding affinity between a ligand and a target protein at the atomic level …

The movable type method applied to protein–ligand binding

Z Zheng, MN Ucisik, KM Merz - Journal of chemical theory and …, 2013 - ACS Publications
Accurately computing the free energy for biological processes like protein folding or protein–
ligand association remains a challenging problem. Both describing the complex …

Mapping enzyme-substrate interactions: Its potential to study the mechanism of enzymes

S Roda, G Santiago, V Guallar - … in Protein Chemistry and Structural Biology, 2020 - Elsevier
With the increase of the need to use more sustainable processes for the industry in our
society, the modeling of enzymes has become crucial to fully comprehend their mechanism …

Yada: a novel tool for molecular docking calculations

S Piotto, L Di Biasi, R Fino, R Parisi, L Sessa… - Journal of computer …, 2016 - Springer
Molecular docking is a computational method employed to estimate the binding between a
small ligand (the drug candidate) and a protein receptor that has become a standard part of …

Generation of pairwise potentials using multidimensional data mining

Z Zheng, J Pei, N Bansal, H Liu, LF Song… - Journal of Chemical …, 2018 - ACS Publications
The rapid development of molecular structural databases provides the chemistry community
access to an enormous array of experimental data that can be used to build and validate …

Crystal structure of SsfS6, the putative C‐glycosyltransferase involved in SF2575 biosynthesis

F Wang, M Zhou, S Singh… - Proteins: Structure …, 2013 - Wiley Online Library
The molecule known as SF2575 from Streptomyces sp. is a tetracycline polyketide natural
product that displays antitumor activity against murine leukemia P388 in vivo. In the SF2575 …

In silico evidence of bitopertin's broad interactions within the SLC6 transporter family

GA de Carvalho, PM Tambwe… - Journal of Pharmacy …, 2024 - academic.oup.com
Abstract The Glycine Transporter Type 1 (GlyT1) significantly impacts central nervous
system functions, influencing glycinergic and glutamatergic neurotransmission. Bitopertin …

Prediction of substrates for glutathione transferases by covalent docking

GQ Dong, S Calhoun, H Fan… - Journal of chemical …, 2014 - ACS Publications
Enzymes in the glutathione transferase (GST) superfamily catalyze the conjugation of
glutathione (GSH) to electrophilic substrates. As a consequence they are involved in a …

Overview of free software developed for designing drugs based on protein-small molecules interaction

P Agrawal, PK Raghav, S Bhalla… - Current Topics in …, 2018 - ingentaconnect.com
One of the fundamental challenges in designing drug molecule against a disease target or
protein is to predict binding affinity between target and drug or small molecule. In this review …

Evaluation of 11 scoring functions performance on matrix metalloproteinases

J Shamsara - International Journal of Medicinal Chemistry, 2014 - Wiley Online Library
Matrix metalloproteinases (MMPs) have distinctive roles in various physiological and
pathological processes such as inflammatory diseases and cancer. This study explored the …