Publications related to Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study

Related publications (33)

Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery

G protein-coupled receptors (GPCRs) are the largest human membrane protein family that transduce extracellular signals into cellular responses. They are major pharmacological targets, with approximately 26% of marketed drugs targeting GPCRs, primarily at t ...

2025

CementFF4: Formal atomic charge polarizable force field for cementitious systems – Bulk and surface

Tecla Bottinelli Montandon, Karen Scrivener, Paul Bowen, Manuel Cordova, Ziga Casar

A general-purpose formal charge polarizable force field for cementitious systems, CementFF4, is presented. The force field includes the following species: Ca, Si, O, H, Al, Zn, OH− and H2O. The force field is a significant extension of previous force field ...

Pergamon-Elsevier Science Ltd2025

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

EPFL2024

Palladium‐Based Dyotropic Rearrangement Enables A Triple Functionalization of Gem‐Disubstituted Alkenes: An Unusual Fluorolactonization Reaction

Chenxu Liu, Qiang Feng, Jieping Zhu, Qian Wang

We report in this paper a Pd(II)-catalyzed migratory gem-fluorolactonization of ene-carboxylic acids. Reaction of 4-methylenealkanoic acid derivatives with Selectfluor in the presence of Pd(OAc)2 (1.0 mol %) at room temperature affords fluorolactones in go ...

Wiley-VCH Verlag GmbH2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

Live-cell imaging powered by computation

Suliana Manley

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

Nature Portfolio2024

Seebeck Coefficient of Ionic Conductors from Bayesian Regression Analysis

Paolo Pegolo

We propose a novel approach to evaluating the ionic Seebeck coefficient in electrolytes from relatively short equilibrium molecular dynamics simulations, based on the Green-Kubo theory of linear response and Bayesian regression analysis. By exploiting the ...

Amer Chemical Soc2024

Well-Defined Ti Surface Sites in Ziegler-Natta Pre-Catalysts from 47/49Ti Solid-State Nuclear Magnetic Resonance Spectroscopy

Pierrick Berruyer

Treatment of Ziegler-Natta (ZN) catalysts with BCl3 improves their activity by increasing the number of active sites. Here we show how Ti-47/49 solid-state nuclear magnetic resonance (NMR) spectroscopy enables us to understand the electronic structure of t ...

Amer Chemical Soc2024

Thermal transport of glasses via machine learning driven simulations

Federico Grasselli, Paolo Pegolo

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

A diversity-driven discovery of potential nanoporous materials for energy-related applications

Sauradeep Majumdar

The design and discovery of potential novel materials is critical for the advancement of climate change mitigation technologies. In this respect, metal-organic frameworks (MOFs) have received considerable attention over the last two decades. The combinatio ...

EPFL2024

Augmenting large language models with chemistry tools

Andres Camilo Marulanda Bran, Carlo Baldassari, Philippe Schwaller, Oliver Tobias Schilter

Large language models (LLMs) have shown strong performance in tasks across domains but struggle with chemistry-related problems. These models also lack access to external knowledge sources, limiting their usefulness in scientific applications. We introduce ...

Nature Portfolio2024

Chalcogen bonding catalysis

Jieping Zhu

Catalysts play a major role in chemical synthesis, and catalysis is considered to be a green and economic process. Catalysis is dominated by covalent interactions between the catalyst and substrate. The design of non-covalent catalysts came into limelight ...

Royal Society of Chemistry2024

Hausdorff dimension of fermions on a random lattice

Mattia Guerino Varrone

Geometric properties of lattice quantum gravity in two dimensions are studied numerically via Monte Carlo on Euclidean Dynamical Triangulations. A new computational method is proposed to simulate gravity coupled with fermions, which allows the study of int ...

Elsevier2024

pyCSH: Automated atomic-level structure generation of bulk C-S-H and investigation of their intrinsic properties

Karen Scrivener, Paul Bowen, Ziga Casar

A new Python code for the automated generation of realistic bulk calcium silicate hydrate (C-S-H) structures is introduced. The code was used to generate 400 structures with Ca/Si of 1.3, 1.5, 1.7, and 1.9. The generated structures are in excellent agreeme ...

Pergamon-Elsevier Science Ltd2024

Orchestrating chromosome conformation capture analysis with Bioconductor

Cyril Matthey-Doret

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Martin Peter Bircher, Justin Villard

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023