Water molecules at protein–drug interfaces: computational prediction and analysis methods

ML Samways, RD Taylor, HEB Macdonald… - Chemical Society …, 2021 - pubs.rsc.org
The fundamental importance of water molecules at drug–protein interfaces is now widely
recognised and a significant feature in structure-based drug design. Experimental methods …

Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory

D Roy, A Kovalenko - International Journal of Molecular Sciences, 2021 - mdpi.com
The statistical mechanics-based 3-dimensional reference interaction site model with the
Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an …

Lin_F9: a linear empirical scoring function for protein–ligand docking

C Yang, Y Zhang - Journal of chemical information and modeling, 2021 - ACS Publications
Molecular docking is one of the most widely used computational tools in structure-based
drug design and is critically dependent on accuracy and robustness of the scoring function …

Secondary structure and conformational stability of the antigen residues making contact with antibodies

X Qiao, L Qu, Y Guo, T Hoshino - The Journal of Physical …, 2021 - ACS Publications
Antibodies are crucial biomolecules that bring high therapeutic efficacy in medicine and
accurate molecular detection in diagnosis. Many studies have been devoted to analyzing …

Analysis of binding modes of antigen–antibody complexes by molecular mechanics calculation

L Qu, X Qiao, F Qi, N Nishida… - Journal of Chemical …, 2021 - ACS Publications
Antibodies are one of the most important protein molecules in biopharmaceutics. Due to the
recent advance in technology for producing monoclonal antibodies, many structural data are …

GalaxyWater-wKGB: prediction of water positions on protein structure using wKGB statistical potential

L Heo, S Park, C Seok - Journal of Chemical Information and …, 2021 - ACS Publications
Proteins fold and function in water, and protein–water interactions play important roles in
protein structure and function. In computational studies on protein structure and interaction …

Accurate prediction of hydration sites of proteins using energy model with atom embedding

P Huang, H Xing, X Zou, Q Han, K Liu, X Sun… - Frontiers in Molecular …, 2021 - frontiersin.org
We propose a method based on neural networks to accurately predict hydration sites in
proteins. In our approach, high-quality data of protein structures are used to parametrize our …

[PDF][PDF] Design and in silico study of the novel small molecular mdm2 inhibitors

CJ Gohil, MN Noolvi - Biointerface Res. Appl. Chem, 2021 - biointerfaceresearch.com
Protein-protein Interaction (PPIs) plays a central role in many diseased conditions. Therefore
to target and to modulate PPIs is an efficient approach for the disease treatment. Cancer is …

Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop

SU Kumar, CGP Doss - Computers in Biology and Medicine, 2021 - Elsevier
The mutant K-Ras with aberrant signaling is the primary cause of several cancers. The
proposed study investigated the influence of water molecules in K-Ras crystal structure …

Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods

NI Giritlioglu, GK Kucuk - bioRxiv, 2021 - biorxiv.org
ABSTRACT COVID-19 is a viral disease that has been a threat to the whole world since
2019. Although effective vaccines against the disease have been developed, there are still …