Water molecules at protein–drug interfaces: computational prediction and analysis methods
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 …
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 …
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
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 …
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 …
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 …
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
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 …
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 …
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 …
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
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 …
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 …
2019. Although effective vaccines against the disease have been developed, there are still …