Principles of docking: An overview of search algorithms and a guide to scoring functions

I Halperin, B Ma, H Wolfson… - … : Structure, Function, and …, 2002 - Wiley Online Library
The docking field has come of age. The time is ripe to present the principles of docking,
reviewing the current state of the field. Two reasons are largely responsible for the maturity …

Epitope mapping: the first step in developing epitope-based vaccines

JM Gershoni, A Roitburd-Berman, DD Siman-Tov… - BioDrugs, 2007 - Springer
Antibodies are an effective line of defense in preventing infectious diseases. Highly potent
neutralizing antibodies can intercept a virus before it attaches to its target cell and, thus …

Toward selective histone deacetylase inhibitor design: homology modeling, docking studies, and molecular dynamics simulations of human class I histone …

DF Wang, P Helquist, NL Wiech… - Journal of medicinal …, 2005 - ACS Publications
Histone deacetylases (HDACs) play an important role in gene transcription. Inhibitors of
HDACs induce cell differentiation and suppress cell proliferation in tumor cells. Although …

Synthesis, experimental, theoretical study and molecular docking of 1-ethylpiperazine-1, 4-diium bis (nitrate)

S Gatfaoui, A Sagaama, N Issaoui, T Roisnel… - Solid State …, 2020 - Elsevier
The present work undertakes the study of a new hybrid material C 6 H 16 N 2 (NO 3) 2
symbolized as follows 1EPBN (1-Ethylpiperazine-1, 4-diium Bis (Nitrate)), a synergy …

On the function of the 14 Å long internal cavity of histone deacetylase-like protein: implications for the design of histone deacetylase inhibitors

DF Wang, O Wiest, P Helquist… - Journal of medicinal …, 2004 - ACS Publications
Histone deacetylases (HDACs) play an important role in gene transcription. Inhibitors of
HDACs induce cell differentiation and suppress cell proliferation in tumor cells. AutoDock …

Reverse vaccinology and its applications

AM Kanampalliwar - Immunoinformatics, 2020 - Springer
The application of the fields of pharmacogenomics and pharmacogenetics to vaccine
design, profoundly combined with bioinformatics, has been recently termed “vaccinomics.” …

Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations

H Liu, LT Da, Y Liu - Biochemical and Biophysical Research …, 2019 - Elsevier
Abstract Taste receptor T1R1-T1R3 can be activated by binding to several natural ligands,
eg, l-glutamate and 5′-ribonucleotides etc., thereby stimulating the umami taste. The …

Protein–protein docking dealing with the unknown

IS Moreira, PA Fernandes… - Journal of computational …, 2010 - Wiley Online Library
Protein–protein binding is one of the critical events in biology, and knowledge of proteic
complexes three‐dimensional structures is of fundamental importance for the biochemical …

Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff

AK Nivedha, S Makeneni, BL Foley… - Journal of …, 2014 - Wiley Online Library
Docking algorithms that aim to be applicable to a broad range of ligands suffer reduced
accuracy because they are unable to incorporate ligand‐specific conformational energies …

A class of biocompatible dye–protein complex optical nanoprobes

X Wang, X Wang, B Qu, N Alifu, J Qi, R Liu, Q Fu… - ACS …, 2021 - ACS Publications
Molecular organic dyes are classic fluorescent nanoprobes finding tremendous uses in
biological and life sciences. Yet, they suffer from low brightness, poor photostability, and lack …