[PDF][PDF] An extensive survey of molecular docking tools and their applications using text mining and deep curation strategies.

K Rawal, T Khurana, H Sharma, S Verma, S Gupta… - PeerJ Preprints, 2019 - peerj.com
The technology of docking molecules in-silico has evolved significantly in recent years and
has become a crucial component of the drug discovery tool process that includes virtual …

General prediction of peptide-MHC binding modes using incremental docking: a proof of concept

DA Antunes, D Devaurs, M Moll, G Lizée, LE Kavraki - Scientific reports, 2018 - nature.com
The class I major histocompatibility complex (MHC) is capable of binding peptides derived
from intracellular proteins and displaying them at the cell surface. The recognition of these …

Carbohydrate self‐assembly at surfaces: STM imaging of sucrose conformation and ordering on Cu (100)

S Abb, N Tarrat, J Cortés, B Andriyevsky… - Angewandte …, 2019 - Wiley Online Library
Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and
assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling …

DeepTPpred: A deep learning approach with matrix factorization for predicting therapeutic peptides by integrating length information

Z Cui, SG Wang, Y He, ZH Chen… - IEEE Journal of …, 2023 - ieeexplore.ieee.org
The abuse of traditional antibiotics has led to increased resistance of bacteria and viruses.
Efficient therapeutic peptide prediction is critical for peptide drug discovery. However, most …

Prediction and clarification of structures of (bio) molecules on surfaces

JC Schön, C Oligschleger, J Cortes - Zeitschrift für Naturforschung B, 2016 - degruyter.com
The design of future materials for biotechnological applications via deposition of molecules
on surfaces will require not only exquisite control of the deposition procedure, but of equal …

IGLOO: An Iterative Global Exploration and Local Optimization Algorithm to Find Diverse Low-Energy Conformations of Flexible Molecules

W Margerit, A Charpentier, C Maugis-Rabusseau… - Algorithms, 2023 - mdpi.com
The exploration of the energy landscape of a chemical system is essential for understanding
and predicting its observable properties. In most cases, this is a challenging task due to the …

Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu (100)

S Abb, N Tarrat, J Cortés, B Andriyevsky, L Harnau… - RSC …, 2019 - pubs.rsc.org
Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little
is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition …

Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of …

V Milia, N Tarrat, C Zanon, J Cortés… - Journal of Chemical …, 2024 - ACS Publications
Exploring the global energy landscape of relatively large molecules at the quantum level is a
challenging problem. In this work, we report the coupling of a nonredundant conformational …

Coarse-grained conformational sampling of protein structure improves the fit to experimental hydrogen-exchange data

D Devaurs, DA Antunes, M Papanastasiou… - Frontiers in molecular …, 2017 - frontiersin.org
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution
produces experimental data that translates into valuable information about the protein's …

Exhaustive exploration of the conformational landscape of small cyclic peptides using a robotics approach

M Jusot, D Stratmann, M Vaisset… - Journal of chemical …, 2018 - ACS Publications
Small cyclic peptides represent a promising class of therapeutic molecules with unique
chemical properties. However, the poor knowledge of their structural characteristics makes …