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International Journal of Molecular Sciences, ISSN 1661-6596, 06/2016, Volume 17, Issue 6
Journal Article
Physical chemistry chemical physics : PCCP, ISSN 1463-9076, 08/2014, Volume 16, Issue 31, pp. 16719 - 16729
By using different evaluation strategies, we systemically evaluated the performance of Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and... 
Ligands | Reproducibility of Results | Databases, Protein | Molecular Conformation | Molecular Dynamics Simulation
Journal Article
Physical Chemistry Chemical Physics, ISSN 1463-9076, 07/2014, Volume 16, Issue 31, pp. 16719 - 16729
Journal Article
Bioorganic & Medicinal Chemistry, ISSN 0968-0896, 10/2019, Volume 27, Issue 19, p. 115052
The human complement fragment 5a ( C5a) is an extremely potent proinflammatory glycoprotein, which upon binding to C5aR triggers a plethora of immune and... 
Neutraligands | Drug repositioning | Fluorescence | Molecular dynamics | MM-PBSA | Raloxifene | Anaphylatoxin | Chemoinformatics | C5a | Circular dichroism
Journal Article
Molecular Informatics, ISSN 1868-1743, 02/2012, Volume 31, Issue 2, pp. 114 - 122
Detailed knowledge of how molecules recognize interaction partners and of the conformational preferences of biomacromolecules is pivotal for understanding... 
Molecular recognition | MM-PBSA | Implicit solvent | Drug design | Binding affinity | PROTEIN-LIGAND BINDING | COMPLEX | CHEMISTRY, MEDICINAL | DOCKING | SOLVATION MODELS | DYNAMICS SIMULATIONS | CONTINUUM SOLVENT | MATHEMATICAL & COMPUTATIONAL BIOLOGY | AFFINITIES | RAS-RAF
Journal Article
Physical Chemistry Chemical Physics, ISSN 1463-9076, 09/2014, Volume 16, Issue 40, pp. 22035 - 22045
With the rapid development of computational techniques and hardware, more rigorous and precise theoretical models have been used to predict the binding... 
Tyrosine | Dielectric constant | Accuracy | Computer simulation | Docking | Mathematical models | Computational efficiency | Kinases
Journal Article
Acta Chimica Slovenica, ISSN 1318-0207, 06/2019, Volume 66, Issue 2, pp. 395 - 401
Binary (nucleotide-protein dimer and hexamer complexes) and ternary (nucleotide-protein-inhibitor complexes) p97 complexes were subjected to molecular dynamics... 
protein protein interactions | mm-pbsa | Drug design | molecular dynamics
Journal Article
Biophysical Chemistry, ISSN 0301-4622, 10/2019, Volume 253, p. 106220
Stabilization of G-quadruplex structures in the c-KIT promoter with the aid of ligands has become an area of great interest in potential cancer therapeutics.... 
MD simulation | MM-PBSA | Quinazolinone derivatives | π-π stacking | Hydrogen bonding | G-quadruplex
Journal Article
Current medicinal chemistry, 05/2018
The inclusion of direct effects mediated by water during the ligand-receptor recognition is a hot-topic of modern computational chemistry applied to drug... 
Journal Article
Journal of Molecular Graphics and Modelling, ISSN 1093-3263, 06/2017, Volume 74, pp. 177 - 192
DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its... 
Fullerene | Molecular dynamics | MM–PBSA calculations | Clustering | DNA | NICS
Journal Article
Chemical Physics Letters, ISSN 0009-2614, 05/2019, Volume 723, pp. 1 - 10
Designed inhibitors of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase from previous experiments show high binding affinities. In this work, the binding... 
DESIGN | PROTEIN | VARIANCE MINIMIZATION | ENTROPY-ENTHALPY COMPENSATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | HMG-COA REDUCTASE | CHEMISTRY, PHYSICAL | MM-PBSA | CRYSTAL | ADAPTIVE SAMPLING REGIME | SOLVATION | Hydrogen | Analysis | Thiols
Journal Article