Search Results - "Devaurs, Didier"

DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach by Antunes, Dinler A, Moll, Mark, Devaurs, Didier, Jackson, Kyle R, Lizée, Gregory, Kavraki, Lydia E

“…Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and…”
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Computational analysis of complement inhibitor compstatin using molecular dynamics by Devaurs, Didier, Antunes, Dinler A., Kavraki, Lydia E.

“…The complement system plays a major role in human immunity, but its abnormal activation can have severe pathological impacts. By mimicking a natural mechanism…”
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3pHLA-score improves structure-based peptide-HLA binding affinity prediction by Conev, Anja, Devaurs, Didier, Rigo, Mauricio Menegatti, Antunes, Dinler Amaral, Kavraki, Lydia E.

“…Binding of peptides to Human Leukocyte Antigen (HLA) receptors is a prerequisite for triggering immune response. Estimating peptide-HLA (pHLA) binding is…”
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Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes by Antunes, Dinler A, Abella, Jayvee R, Devaurs, Didier, Rigo, Maurício M, Kavraki, Lydia E

“…Understanding the mechanisms involved in the activation of an immune response is essential to many fields in human health, including vaccine development and…”
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Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data by Devaurs, Didier, Antunes, Dinler A, Kavraki, Lydia E

“…Both experimental and computational methods are available to gather information about a protein's conformational space and interpret changes in protein…”
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A multi-tree extension of the transition-based RRT: Application to ordering-and-pathfinding problems in continuous cost spaces by Devaurs, Didier, Simeon, Thierry, Cortes, Juan

“…The Transition-based RRT (T-RRT) is a variant of RRT developed for path planning on a continuous cost space, i.e. a configuration space featuring a continuous…”
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Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins by Devaurs, Didier, Antunes, Dinler A, Hall-Swan, Sarah, Mitchell, Nicole, Moll, Mark, Lizée, Gregory, Kavraki, Lydia E

“…Docking large ligands, and especially peptides, to protein receptors is still considered a challenge in computational structural biology. Besides the issue of…”
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Optimal Path Planning in Complex Cost Spaces With Sampling-Based Algorithms by Devaurs, Didier, Simeon, Thierry, Cortes, Juan

“…Sampling-based algorithms for path planning, such as the Rapidly-exploring Random Tree (RRT), have achieved great success, thanks to their ability to…”
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Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data by Devaurs, Didier, Antunes, Dinler A, Borysik, Antoni J

“…Data produced by hydrogen-exchange monitoring experiments have been used in structural studies of molecules for several decades. Despite uncertainties about…”
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Understanding the challenges of protein flexibility in drug design by Antunes, Dinler A, Devaurs, Didier, Kavraki, Lydia E

“…Protein-ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug…”
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General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept by Antunes, Dinler A., Devaurs, Didier, Moll, Mark, Lizée, Gregory, Kavraki, Lydia E.

“…The class I major histocompatibility complex (MHC) is capable of binding peptides derived from intracellular proteins and displaying them at the cell surface…”
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A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction by Kravchenko, Oleksandr, Varava, Anastasiia, Pokorny, Florian T, Devaurs, Didier, Kavraki, Lydia E, Kragic, Danica

“…We define a molecular caging complex as a pair of molecules in which one molecule (the “host” or “cage”) possesses a cavity that can encapsulate the other…”
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Species abundance patterns in an ecosystem simulation studied through Fisher’s logseries by Devaurs, Didier, Gras, Robin

“…We have developed an individual-based evolving predator–prey ecosystem simulation that integrates, for the first time, a complex individual behaviour model, an…”
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DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins by Hall-Swan, Sarah, Devaurs, Didier, Rigo, Mauricio M., Antunes, Dinler A., Kavraki, Lydia E., Zanatta, Geancarlo

“…An unprecedented research effort has been undertaken in response to the ongoing COVID-19 pandemic. This has included the determination of hundreds of…”
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EnGens: a computational framework for generation and analysis of representative protein conformational ensembles by Conev, Anja, Rigo, Mauricio Menegatti, Devaurs, Didier, Fonseca, André Faustino, Kalavadwala, Hussain, de Freitas, Martiela Vaz, Clementi, Cecilia, Zanatta, Geancarlo, Antunes, Dinler Amaral, Kavraki, Lydia E

“…Abstract Proteins are dynamic macromolecules that perform vital functions in cells. A protein structure determines its function, but this structure is not…”
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An individual-based evolving predator-prey ecosystem simulation using a fuzzy cognitive map as the behavior model by Gras, Robin, Devaurs, Didier, Wozniak, Adrianna, Aspinall, Adam

“…We present an individual-based predator-prey model with, for the first time, each agent behavior being modeled by a fuzzy cognitive map (FCM), allowing the…”
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MoMA-LigPath: a web server to simulate protein-ligand unbinding by Devaurs, Didier, Bouard, Léa, Vaisset, Marc, Zanon, Christophe, Al-Bluwi, Ibrahim, Iehl, Romain, Siméon, Thierry, Cortés, Juan

“…Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity…”
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Defining Low-Dimensional Projections to Guide Protein Conformational Sampling by Novinskaya, Anastasia, Devaurs, Didier, Moll, Mark, Kavraki, Lydia E

“…Exploring the conformational space of proteins is critical to characterize their functions. Numerous methods have been proposed to sample a protein's…”
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Parallelizing RRT on Large-Scale Distributed-Memory Architectures by Devaurs, D., Simeon, T., Cortes, J.

“…This paper addresses the problem of parallelizing the Rapidly-exploring Random Tree (RRT) algorithm on large-scale distributed-memory architectures, using the…”
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HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy by Antunes, Dinler A, Abella, Jayvee R, Hall-Swan, Sarah, Devaurs, Didier, Conev, Anja, Moll, Mark, Lizée, Gregory, Kavraki, Lydia E

“…HLA protein receptors play a key role in cellular immunity. They bind intracellular peptides and display them for recognition by T-cell lymphocytes. Because…”
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