Improvement of conventional anti-cancer drugs as new tools against multidrug resistant tumors

S Dallavalle, V Dobričić, L Lazzarato, E Gazzano… - Drug Resistance …, 2020 - Elsevier
Multidrug resistance (MDR) is the dominant cause of the failure of cancer chemotherapy.
The design of antitumor drugs that are able to evade MDR is rapidly evolving, showing that …

Advances in molecular dynamics simulations and enhanced sampling methods for the study of protein systems

R Lazim, D Suh, S Choi - International journal of molecular sciences, 2020 - mdpi.com
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

[HTML][HTML] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

Large-scale assessment of binding free energy calculations in active drug discovery projects

CEM Schindler, H Baumann, A Blum… - Journal of Chemical …, 2020 - ACS Publications
Accurate ranking of compounds with regards to their binding affinity to a protein using
computational methods is of great interest to pharmaceutical research. Physics-based free …

Atomistic modeling of electrocatalysis: Are we there yet?

N Abidi, KRG Lim, ZW Seh… - Wiley Interdisciplinary …, 2021 - Wiley Online Library
Electrified interfaces play a prime role in energy technologies, from batteries and capacitors
to heterogeneous electrocatalysis. The atomistic understanding and modeling of these …

CHARMM at 45: Enhancements in accessibility, functionality, and speed

W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Assessing developability early in the discovery process for novel biologics

ML Fernández-Quintero, A Ljungars, F Waibl, V Greiff… - MAbs, 2023 - Taylor & Francis
Beyond potency, a good developability profile is a key attribute of a biological drug.
Selecting and screening for such attributes early in the drug development process can save …

Simulation studies of amyloidogenic polypeptides and their aggregates

IM Ilie, A Caflisch - Chemical reviews, 2019 - ACS Publications
Amyloids, fibrillar assembly of (poly) peptide chains, are associated with neurodegenerative
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …

Integrating Computation, Experiment, and Machine Learning in the Design of Peptide‐Based Supramolecular Materials and Systems

M Ramakrishnan, A van Teijlingen… - Angewandte Chemie …, 2023 - Wiley Online Library
Interest in peptide‐based supramolecular materials has grown extensively since the 1980s
and the application of computational methods has paralleled this. These methods contribute …

Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules

K Świderek, S Velasco-Lozano, MÀ Galmés… - Nature …, 2023 - nature.com
Biocatalysis is a key technology enabling plastic recycling. However, despite advances
done in the development of plastic-degrading enzymes, the molecular mechanisms that …