Pragmatic coarse-graining of proteins: models and applications

L Borges-Araújo, I Patmanidis, AP Singh… - Journal of Chemical …, 2023 - ACS Publications
The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

[HTML][HTML] Comparison of the binding energies of approved mpox drugs and phytochemicals through molecular docking, molecular dynamics simulation, and ADMET …

RK Mohapatra, A Mahal, A Ansari, M Kumar… - Journal of Biosafety and …, 2023 - Elsevier
The mpox (previously monkeypox) outbreak in more than 100 non-endemic countries in
2022 posed a serious global health concern. Mpox is emerging as a global public health …

Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants

W Shinoda, R DeVane, ML Klein - Molecular Simulation, 2007 - Taylor & Francis
A new systematic approach to build coarse-grained (CG) molecular models for
surfactants/water systems is proposed. A step-by-step approach using several molecular …

Cyclohexane-1, 3-dione derivatives as future therapeutic agents for NSCLC: QSAR modeling, in silico ADME-Tox properties, and structure-based drug designing …

O Daoui, S Elkhattabi, M Bakhouch, S Belaidi… - ACS …, 2023 - ACS Publications
The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of
several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this …

Docking studies and molecular dynamics simulation of triazole benzene sulfonamide derivatives with human carbonic anhydrase IX inhibition activity

P Gopinath, MK Kathiravan - RSC advances, 2021 - pubs.rsc.org
Carbonic anhydrase IX has been used as a hypoxia endogenous marker in a range of solid
tumors including renal cell, lung, bladder and tumors of the head and neck. α-CA IX isozyme …

Computational identification of 2, 4-disubstituted amino-pyrimidines as L858R/T790M-EGFR double mutant inhibitors using pharmacophore map**, molecular …

R Pawara, I Ahmad, S Surana, H Patel - In Silico Pharmacology, 2021 - Springer
Pharmacophore modelling studies have been performed for a series of 2, 4-disubstituted-
pyrimidines derivatives as EGFR L858R/T790M tyrosine kinase inhibitors. The high scoring …

Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field

W Shinoda, R DeVane, ML Klein - The Journal of Physical …, 2010 - ACS Publications
A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic
lipids. The model is an extension of our previous work on nonionic surfactants and is …

Compounds Identified from Marine Mangrove Plant (Avicennia alba) as Potential Antiviral Drug Candidates against WDSV, an In-Silico Approach

MO Aljahdali, MHR Molla, F Ahammad - Marine Drugs, 2021 - mdpi.com
Walleye dermal sarcoma virus (WDSV) is a type of retrovirus, which affects most of the adult
walleye fishes during the spawning time. The virus causes multiple epithelial tumors on the …

Coarse-grained molecular modeling of non-ionic surfactant self-assembly

W Shinoda, R DeVane, ML Klein - Soft Matter, 2008 - pubs.rsc.org
A coarse-grained (CG) molecular model for nonionic surfactants is presented. The
transferability and versatility are demonstrated by applying the model to the bulk aqueous …

In vitro and in silico analysis of Thymus serpyllum essential oil as bioactivity enhancer of antibacterial and antifungal agents

D Salaria, R Rolta, CN Patel, K Dev… - Journal of …, 2022 - Taylor & Francis
Wild thyme (Thymus serpyllum L.) of family Laminaceae is an unexplored perennial
medicinal shrub. Aerial part of this plant is traditionally used for the treatment of respiratory …