New generation of elastic network models
JR López-Blanco, P Chacón - Current opinion in structural biology, 2016 - Elsevier
Highlights•ENMs efficiently capture the collective functional motions of macromolecules.•The
intrinsic dynamics predictable by ENMs is robust to different coarse-grained …
intrinsic dynamics predictable by ENMs is robust to different coarse-grained …
Quantitatively accounting for protein reorganization in computer-aided drug design
Structure-based drug design frequently operates under the assumption that a single holo
structure is relevant. However, a large number of crystallographic examples clearly show …
structure is relevant. However, a large number of crystallographic examples clearly show …
Computational insights into the conformational accessibility and binding strength of SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2
C Peng, Z Zhu, Y Shi, X Wang, K Mu… - The journal of …, 2020 - ACS Publications
The spike protein of SARS-CoV-2 (CoV-2-S) mediates the virus entry into human cells.
Experimental studies have shown the stronger binding affinity of the RBD (receptor binding …
Experimental studies have shown the stronger binding affinity of the RBD (receptor binding …
Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling
J Chen, J Wang, W Zhu - Physical Chemistry Chemical Physics, 2017 - pubs.rsc.org
The hydrolysis of a β-lactam core ring caused by new Delphi metallo-β-lactamase 1 (NDM-
1) with the help of two zinc cofactors induces significant resistance toward β-lactam …
1) with the help of two zinc cofactors induces significant resistance toward β-lactam …
Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question
because the small molecule occupies both the ATP pocket and the allosteric pocket of the …
because the small molecule occupies both the ATP pocket and the allosteric pocket of the …
Revealing origin of decrease in potency of darunavir and amprenavir against HIV-2 relative to HIV-1 protease by molecular dynamics simulations
J Chen, Z Liang, W Wang, C Yi, S Zhang, Q Zhang - Scientific reports, 2014 - nature.com
Clinical inhibitors Darunavir (DRV) and Amprenavir (APV) are less effective on HIV-2
protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with …
protease (PR2) than on HIV-1 protease (PR1). To identify molecular basis associated with …
Exploring the binding mechanism and accessible angle of SARS-CoV-2 spike and ACE2 by molecular dynamics simulation and free energy calculation
C Peng, Z Zhu, Y Shi, X Wang, K Mu, Y Yang, X Zhang… - 2020 - chemrxiv.org
The SARS-CoV-2 has caused more than 2,000 deaths as of 20 February 2020 worldwide
but there is no approved effective drug. The SARS-CoV-2 spike (S) glycoprotein is a key …
but there is no approved effective drug. The SARS-CoV-2 spike (S) glycoprotein is a key …
Protein interaction evolution from promiscuity to specificity with reduced flexibility in an increasingly complex network
A key question regarding protein evolution is how proteins adapt to the dynamic
environment in which they function and how in turn their evolution shapes the protein …
environment in which they function and how in turn their evolution shapes the protein …
Tackling hysteresis in conformational sampling: how to be forgetful with memento
SM Lichtinger, PC Biggin - Journal of Chemical Theory and …, 2023 - ACS Publications
The structure of proteins has long been recognized to hold the key to understanding and
engineering their function, and rapid advances in structural biology and protein structure …
engineering their function, and rapid advances in structural biology and protein structure …
Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and …
J Chen, J Wang, W Zhu - Physical Chemistry Chemical Physics, 2017 - pubs.rsc.org
Anaplastic lymphoma kinase (ALK) has been regarded as a promising drug target in the
treatment of tumors and the mutation L1196M induces different levels of drug resistance …
treatment of tumors and the mutation L1196M induces different levels of drug resistance …