Insights on peptide topology in the computational design of protein ligands: the example of lysozyme binding peptides

Cristina Cantarutti, M. Cristina Vargas, Cedrix J. Dongmo Foumthuim, Mireille Dumoulin, Sara La Manna, Daniela Marasco, Carlo Santambrogio, Rita Grandori, Giacinto Scoles, Miguel A. Soler, Alessandra Corazza and Sara Fortuna

Phys. Chem. Chem. Phys., 2021, 23, 23158
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Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions

Rika Tandiana, German P. Barletta, Miguel Angel Soler, Sara Fortuna and Walter Rocchia

J. Chem. Theory Comput., 2024, 20, 2630
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Open protocols for docking and MD-based scoring of peptide substrates

Rodrigo Ochoa, Ángel Santiago and Melissa Alegría-Arcos

Artificial Intelligence in the Life Sciences, 2022, 2, 100044
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Mutation Hotspot for Changing the Substrate Specificity of β-N-Acetylhexosaminidase: A Library of GlcNAcases

Pavlína Nekvasilová, Natalia Kulik, Michael Kotik, Lucie Petrásková, Kristýna Slámová, Vladimír Křen and Pavla Bojarová

IJMS, 2022, 23, 12456
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KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability

Carter J. Wilson, Megan Chang, Mikko Karttunen and Wing-Yiu Choy

IJMS, 2021, 22, 5408
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PepFun: Open Source Protocols for Peptide-Related Computational Analysis

Rodrigo Ochoa and Pilar Cossio

Molecules, 2021, 26, 1664
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Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders

Rodrigo Ochoa, Roman A. Laskowski, Janet M. Thornton and Pilar Cossio

Front. Mol. Biosci., 2021, 8
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Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol

Laura Pedraza-González, Leonardo Barneschi, Daniele Padula, Luca De Vico and Massimo Olivucci

Top Curr Chem (Z), 2022, 380
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Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations

Rodrigo Ochoa, Alessandro Laio and Pilar Cossio

J. Chem. Inf. Model., 2019, 59, 3464
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Protocol for iterative optimization of modified peptides bound to protein targets

Rodrigo Ochoa, Pilar Cossio and Thomas Fox

J Comput Aided Mol Des, 2022, 36, 825
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Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study

Khadijeh Ahmadi, Alireza Farasat, Mosayeb Rostamian, Behrooz Johari and Hamid Madanchi

Journal of Biomolecular Structure and Dynamics, 2022, 40, 5566
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PARCE: Protocol for Amino acid Refinement through Computational Evolution

Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio and Pilar Cossio

Computer Physics Communications, 2021, 260, 107716
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The Perovskites MSnO3 (M = Mg, Ca): Ab Initio Investigation of Structural, Electronic, Thermodynamic, and Thermoelectric Characteristics

Y. El-harrar, R. Masrour, M. Hamedoun, J. Kharbach, A. Rezzouk, N. Benzakour and K. Bouslykhane

J Supercond Nov Magn, 2025, 38
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Computational Evolution of Beta-2-Microglobulin Binding Peptides for Nanopatterned Surface Sensors

Abimbola Feyisara Adedeji Olulana, Miguel A. Soler, Martina Lotteri, Hendrik Vondracek, Loredana Casalis, Daniela Marasco, Matteo Castronovo and Sara Fortuna

IJMS, 2021, 22, 812
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Effects of unsaturated fatty acids (Arachidonic/Oleic Acids) on stability and structural properties of Calprotectin using molecular docking and molecular dynamics simulation approach

Nematollah Gheibi, Mohamad Ghorbani, Hanifeh Shariatifar, Alireza Farasat and Eugene A. Permyakov

PLoS ONE, 2020, 15, e0230780
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Systematic Identification and Comparative Analysis of Human Cartilage-Derived Self-peptides Presented Differently by Ankylosing Spondylitis (AS)-Associated HLA-B*27:05 and Non-AS-associated HLA-B*27:09

Chang Ge, Wenzhi Zhang, Rui He and Haiping Cai

Int J Pept Res Ther, 2020, 26, 513
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In silico assessment of human Calprotectin subunits (S100A8/A9) in presence of sodium and calcium ions using Molecular Dynamics simulation approach

Nematollah Gheibi, Mohammad Ghorbani, Hanifeh Shariatifar, Alireza Farasat and Eugene A. Permyakov

PLoS ONE, 2019, 14, e0224095
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Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol

Rodrigo Ochoa, Victoria Alves Santos Lunardelli, Daniela Santoro Rosa, Alessandro Laio and Pilar Cossio

Front. Immunol., 2022, 13
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