Paulo Cesar Telles de Souza

Pós-doutorado

Formação complementar

Idiomas

Áreas de atuação

Organização de eventos

Participação em eventos

Participação em bancas

Orientou

Produções bibliográficas

• DIAMANTI, ELEONORA ; SOUZA, PAULO C. T. ; SETYAWATI, INDA ; BOUSIS, SPYRIDON ; MONJAS, LETICIA ; SWIER, LOTTEKE J.Y.M. ; SHAMS, ATANAZ ; TSARENKO, ALEKSEI ; STANEK, WERONIKA K. ; JÄGER, MANUEL ; MARRINK, SIEWERT J. ; SLOTBOOM, DIRK J. ; HIRSCH, ANNA K. H. . Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications Biology , v. 7, p. 70, 2024.

• PANDEY, MAYANK PRAKASH ; TELLES DE SOUZA, PAULO CESAR ; PEZESHKIAN, WERIA ; KHANDELIA, HIMANSHU . Bending of a lipid membrane edge by annexin A5 trimers. BIOPHYSICAL JOURNAL , v. -, p. 1-9, 2024.

• BORGES-ARAÚJO, LUÍS ; PEREIRA, GILBERTO P. ; VALÉRIO, MARIANA ; SOUZA, PAULO C.T. . Assessing the Martini 3 protein model: A review of its path and potential. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS , v. 1872, p. 141014, 2024.

• PEREIRA, GILBERTO P. ; ALESSANDRI, RICCARDO ; DOMÍNGUEZ, MOISÉS ; ARAYA-OSORIO, ROCÍO ; GRÜNEWALD, LINUS ; BORGES-ARAÚJO, LUÍS ; WU, SANGWOOK ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. ; MERA-ADASME, RAUL . Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics. Journal of Chemical Theory and Computation , v. 20, p. 5763-5773, 2024.

• ALBANI, SIMONE ; ESWARAN, VISHAL SUDHA BHAGAVATH ; PIERGENTILI, ALESSIA ; DE SOUZA, PAULO CESAR TELLES ; LAMPERT, ANGELIKA ; ROSSETTI, GIULIA . Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7. INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES , v. 278, p. 134219, 2024.

• PEDERSEN, KASPER B. ; BORGES-ARAÚJO, LUÍS ; STANGE, AMANDA D. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. ; SCHIØTT, BIRGIT . OLIVES: A Go¿-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field. Journal of Chemical Theory and Computation , v. 20, p. 8049-8070, 2024.

• BARTOCCI, ALESSIO ; GRAZZI, ANDREA ; AWAD, NOUR ; CORRINGER, PIERRE-JEAN ; SOUZA, PAULO C. T. ; CECCHINI, MARCO . A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1. Nature Communications , v. 15, p. 9040, 2024.

• WACLAWIKOVÁ, BARBORA ; CESAR TELLES DE SOUZA, PAULO ; SCHWALBE, MARKUS ; NEOCHORITIS, CONSTANTINOS G. ; HOORNENBORG, WARNER ; NELEMANS, SIEGER A. ; MARRINK, SIEWERT J. ; EL AIDY, SAHAR . Potential binding modes of the gut bacterial metabolite, 5-hydroxyindole, to the intestinal L-type calcium channels and its impact on the microbiota in rats. Gut Microbes , v. 15, p. e2154544, 2023.

• HILPERT, CÉCILE ; BERANGER, LOUIS ; SOUZA, PAULO C. T. ; VAINIKKA, PETTERI A. ; NIETO, VINCENT ; MARRINK, SIEWERT J. ; MONTICELLI, LUCA ; LAUNAY, GUILLAUME . Facilitating CG Simulations with MAD: The MArtini Database Server. Journal of Chemical Information and Modeling , v. 63, p. 702-710, 2023.

• MACCALLUM, JUSTIN L. ; HU, SHANGNONG ; LENZ, STEFAN ; SOUZA, PAULO C.T. ; CORRADI, VALENTINA ; TIELEMAN, D. PETER . An implementation of the Martini coarse-grained force field in OpenMM. BIOPHYSICAL JOURNAL , v. -, p. -, 2023.

• SAHOO, AMITA R. ; SOUZA, PAULO C.T. ; MENG, ZHIYUAN ; BUCK, MATTHIAS . Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer. STRUCTURE , v. 31, p. 735-745.e2, 2023.

• EMPEREUR-MOT, CHARLY ; PEDERSEN, KASPER B. ; CAPELLI, RICCARDO ; CRIPPA, MARTINA ; CARUSO, CRISTINA ; PERRONE, MATTIA ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. ; PAVAN, GIOVANNI M. . Automatic Optimization of Lipid Models in the Martini Force Field Using. Journal of Chemical Information and Modeling , v. 63, p. 3827-3838, 2023.

• THANGARATNARAJAH, CHANCIEVAN ; NIJLAND, MARK ; BORGES-ARAÚJO, LUÍS ; JEUCKEN, AIKE ; RHEINBERGER, JAN ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. ; PAULINO, CRISTINA ; SLOTBOOM, DIRK J. . Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nature Communications , v. 14, p. 4484, 2023.

• DIAMANTI, ELEONORA ; SOUZA, PAULO C. T. ; SETYAWATI, INDA ; BOUSIS, SPYRIDON ; MONJAS, LETICIA ; SWIER, LOTTEKE J.Y.M. ; SHAMS, ATANAZ ; TSARENKO, ALEKSEI ; STANEK, WERONIKA K. ; JÄGER, MANUEL ; MARRINK, SIEWERT J. ; SLOTBOOM, DIRK J. ; HIRSCH, ANNA K. H. . Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Communications Biology , v. 6, p. 1182, 2023.

• INGÓLFSSON, HELGI I. ; RIZUAN, AZAMAT ; LIU, XIKUN ; MOHANTY, PRIYESH ; SOUZA, PAULO C.T. ; MARRINK, SIEWERT J. ; BOWERS, MICHAEL T. ; MITTAL, JEETAIN ; BERRY, JOEL . Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation. BIOPHYSICAL JOURNAL , v. 122, p. 4370-4381, 2023.

• KOUKOS, PANAGIOTIS I. ; DEHGHANI-GHAHNAVIYEH, SEPEHR ; VELEZ-VEGA, CAMILO ; MANCHESTER, JOHN ; TIELEMAN, D. PETER ; DUCA, JOSÉ S. ; SOUZA, PAULO C. T. ; COURNIA, ZOE . Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications. Journal of Chemical Theory and Computation , v. 19, p. 8901-8918, 2023.

• STROH, KAI STEFFEN ; SOUZA, PAULO C. T. ; MONTICELLI, LUCA ; RISSELADA, HERRE JELGER . CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization. Journal of Chemical Theory and Computation , v. 19, p. 8384-8400, 2023.

• BORGES-ARAÚJO, LUÍS ; PATMANIDIS, ILIAS ; SINGH, AKHIL P. ; SANTOS, LUCIANNA H. S. ; SIERADZAN, ADAM K. ; VANNI, STEFANO ; CZAPLEWSKI, CEZARY ; PANTANO, SERGIO ; SHINODA, WATARU ; MONTICELLI, LUCA ; LIWO, ADAM ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. . Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of Chemical Theory and Computation , v. 19, p. 7112-7135, 2023.

• BORGES-ARAÚJO, LUÍS ; BORGES-ARAÚJO, ANA C. ; OZTURK, TUGBA NUR ; RAMIREZ-ECHEMENDIA, DANIEL P. ; FÁBIÁN, BALÁZS ; CARPENTER, TIMOTHY S. ; THALLMAIR, SEBASTIAN ; BARNOUD, JONATHAN ; INGÓLFSSON, HELGI I. ; HUMMER, GERHARD ; TIELEMAN, D. PETER ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. ; MELO, MANUEL N. . Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation , v. 19, p. 7387-7404, 2023.

• PEREIRA, GILBERTO P. ; JIMÉNEZ-GARCÍA, BRIAN ; PELLARIN, RICCARDO ; LAUNAY, GUILLAUME ; WU, SANGWOOK ; MARTIN, JULIETTE ; SOUZA, PAULO C. T. . Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking. Journal of Chemical Information and Modeling , v. 63, p. 6823-6833, 2023.

• ALESSANDRI, RICCARDO ; BARNOUD, JONATHAN ; GERTSEN, ANDERS S. ; PATMANIDIS, ILIAS ; DE VRIES, ALEX H. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . Martini 3 Coarse¿Grained Force Field: Small Molecules. Advanced Theory And Simulations , v. 5, p. 2100391, 2022.

• MACHADO, NEILA ; BRUININKS, BART M. H. ; SINGH, PRIYANKA ; DOS SANTOS, LAURITA ; DAL PIZZOL, CARINE ; DIEAMANT, GUSTAVO DE C. ; KRUGER, ODIVANIA ; MARTIN, AIRTON A. ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. ; FAVERO, PRISCILA P. . Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes. Nanoscale , v. 14, p. 506-514, 2022.

• GRÜNEWALD, FABIAN ; ALESSANDRI, RICCARDO ; Kroon, Peter C. ; MONTICELLI, LUCA ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials. Nature Communications , v. 13, p. 68, 2022.

• PATMANIDIS, ILIAS ; SOUZA, PAULO C. T. ; SAMI, SELIM ; HAVENITH, REMCO W. A. ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. . Modelling structural properties of cyanine dye nanotubes at coarse-grained level. Nanoscale Advances , v. -, p. 1-10, 2022.

• MARRINK, SIEWERT J. ; MONTICELLI, LUCA ; MELO, MANUEL N. ; ALESSANDRI, RICCARDO ; TIELEMAN, D. PETER ; SOUZA, PAULO C. T. . Two decades of Martini: Better beads, broader scope. Wiley Interdisciplinary Reviews-Computational Molecular Science , v. -, p. e1620, 2022.

• KJØLBYE, LISBETH R. ; PEREIRA, GILBERTO P. ; BARTOCCI, ALESSIO ; PANNUZZO, MARTINA ; ALBANI, SIMONE ; MARCHETTO, ALESSANDRO ; JIMÉNEZ-GARCÍA, BRIAN ; MARTIN, JULIETTE ; ROSSETTI, GIULIA ; CECCHINI, MARCO ; WU, SANGWOOK ; MONTICELLI, LUCA ; SOUZA, PAULO C. T. . Towards design of drugs and delivery systems with the Martini coarse-grained model. QRB Discovery , v. 3, p. e19, 2022.

• GRÜNEWALD, FABIAN ; PUNT, MATS H. ; JEFFERYS, ELIZABETH E. ; VAINIKKA, PETTERI A. ; KÖNIG, MELANIE ; VIRTANEN, VALTTERI ; MEYER, TRAVIS A. ; PEZESHKIAN, WERIA ; GORMLEY, ADAM J. ; KARONEN, MAARIT ; SANSOM, MARK S. P. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . Martini 3 Coarse-Grained Force Field for Carbohydrates. Journal of Chemical Theory and Computation , v. 18, p. 7555-7569, 2022.

• SOUZA, PAULO C. T. ; LIMONGELLI, VITTORIO ; WU, SANGWOOK ; MARRINK, SIEWERT J. ; MONTICELLI, LUCA . Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. FRONTIERS IN MOLECULAR BIOSCIENCES , v. 8, p. 1-9, 2021.

• TSANAI, MARIA ; FREDERIX, PIM W. J. M. ; SCHROER, CARSTEN F. E. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model. Chemical Science , v. 12, p. 8521-8530, 2021.

• WESTERFIELD, JUSTIN M. ; SAHOO, AMITA R. ; ALVES, DAIANE S. ; GRAU, BRAYAN ; CAMERON, ALAYNA ; MAXWELL, MIKAYLA ; SCHUSTER, JENNIFER A. ; SOUZA, PAULO C.T. ; MINGARRO, ISMAEL ; BUCK, MATTHIAS ; BARRERA, FRANCISCO N. . Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. JOURNAL OF MOLECULAR BIOLOGY , v. 433, p. 167144, 2021.

• LIACI, A. MANUEL ; STEIGENBERGER, BARBARA ; TELLES DE SOUZA, PAULO CESAR ; TAMARA, SEM ; GRÖLLERS-MULDERIJ, MARISKA ; OGRISSEK, PATRICK ; MARRINK, SIEWERT J. ; SCHELTEMA, RICHARD A. ; FÖRSTER, FRIEDRICH . Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. MOLECULAR CELL , p. 1?15, 2021.

• SOUZA, PAULO C. T. ; ALESSANDRI, RICCARDO ; BARNOUD, JONATHAN ; THALLMAIR, SEBASTIAN ; FAUSTINO, IGNACIO ; GRÜNEWALD, FABIAN ; PATMANIDIS, ILIAS ; ABDIZADEH, HALEH ; BRUININKS, BART M. H. ; WASSENAAR, TSJERK A. ; Kroon, Peter C. ; MELCR, JOSEF ; NIETO, VINCENT ; CORRADI, VALENTINA ; KHAN, HANIF M. ; DOMA'SKI, JAN ; JAVANAINEN, MATTI ; MARTINEZ-SEARA, HECTOR ; REUTER, NATHALIE ; BEST, ROBERT B. ; et.al . Martini 3: a general purpose force field for coarse-grained molecular dynamics. NATURE METHODS , v. 18, p. 382?388, 2021.

• BRUININKS, BART M. H. ; THIE, ALBERT S. ; SOUZA, PAULO C. T. ; WASSENAAR, TSJERK A. ; FARAJI, SHIRIN ; MARRINK, SIEWERT J. . Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies. Journal of Chemical Theory and Computation , v. 17, p. 7873-7885, 2021.

• VAINIKKA, PETTERI ; THALLMAIR, SEBASTIAN ; SOUZA, PAULO CESAR TELLES ; MARRINK, SIEWERT J. . Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties. ACS Sustainable Chemistry & Engineering , v. 9, p. 17338-17350, 2021.

• ZHANG, SHENGLI ; HUANG, GANG ; VERSLOOT, RODERICK CORSTIAAN ABRAHAM ; BRUININKS, BART MARLON HERWIG ; DE SOUZA, PAULO CESAR TELLES ; MARRINK, SIEWERT-JAN ; MAGLIA, GIOVANNI . Bottom-up fabrication of a proteasome-nanopore that unravels and processes single proteins. Nature Chemistry , v. 13, p. 1192-1199, 2021.

• BORGES-ARAÚJO, LUÍS ; SOUZA, PAULO C. T. ; FERNANDES, FÁBIO ; MELO, MANUEL N. . Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field. Journal of Chemical Theory and Computation , v. 18, p. 357-373, 2021.

• FAUSTINO, IGNACIO ; ABDIZADEH, HALEH ; SOUZA, PAULO C. T. ; JEUCKEN, AIKE ; STANEK, WERONIKA K. ; GUSKOV, ALBERT ; SLOTBOOM, DIRK J. ; MARRINK, SIEWERT J. . Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nature Communications , v. 11, p. 1763, 2020.

• KHAN, HANIF M. ; SOUZA, PAULO C. T. ; THALLMAIR, SEBASTIAN ; BARNOUD, JONATHAN ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. ; REUTER, NATHALIE . Capturing Choline-Aromatics Cation−π Interactions in the MARTINI Force Field. Journal of Chemical Theory and Computation , v. 16, p. 2550-2560, 2020.

• BRUININKS, BART MH ; SOUZA, PAULO CT ; INGOLFSSON, HELGI ; MARRINK, SIEWERT J . A molecular view on the escape of lipoplexed DNA from the endosome. eLife , v. 9, p. e52012, 2020.

• GRÜNEWALD, FABIAN ; SOUZA, PAULO C. T. ; ABDIZADEH, HALEH ; BARNOUD, JONATHAN ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. . Titratable Martini model for constant pH simulations. JOURNAL OF CHEMICAL PHYSICS , v. 153, p. 024118, 2020.

• SOUZA, PAULO C. T. ; THALLMAIR, SEBASTIAN ; CONFLITTI, PAOLO ; RAMÍREZ-PALACIOS, CARLOS ; ALESSANDRI, RICCARDO ; RANIOLO, STEFANO ; LIMONGELLI, VITTORIO ; MARRINK, SIEWERT J. . Protein-ligand binding with the coarse-grained Martini model. Nature Communications , v. 11, p. 3714, 2020.

• VAZQUEZ-SALAZAR, LUIS ITZA ; SELLE, MICHELE ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. ; SOUZA, PAULO C. T. . Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction. GREEN CHEMISTRY , v. 22, p. 7376-7386, 2020.

• BONDARENKO, ANNA S. ; PATMANIDIS, ILIAS ; ALESSANDRI, RICCARDO ; SOUZA, PAULO C. T. ; JANSEN, THOMAS L. C. ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. ; KNOESTER, JASPER . Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates. Chemical Science , v. 11, p. 11514-11524, 2020.

• MARRINK, SIEWERT J. ; CORRADI, VALENTINA ; SOUZA, PAULO C.T. ; INGÓLFSSON, HELGI I. ; TIELEMAN, D. PETER ; SANSOM, MARK S.P. . Computational Modeling of Realistic Cell Membranes. CHEMICAL REVIEWS , v. 119, p. 6184-6226, 2019.

• ALESSANDRI, RICCARDO ; SOUZA, PAULO C. T. ; THALLMAIR, SEBASTIAN ; MELO, MANUEL N. ; DE VRIES, ALEX H. ; MARRINK, SIEWERT J. . Pitfalls of the Martini Model. Journal of Chemical Theory and Computation , v. 15, p. 5448-5460, 2019.

• SOUZA, PAULO C. T. ; THALLMAIR, SEBASTIAN ; MARRINK, SIEWERT J. ; MERA-ADASME, RAÚL . An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation. Journal of Physical Chemistry Letters , v. 10, p. 7740-7744, 2019.

• LIU, JIAN ; QIU, LI ; ALESSANDRI, RICCARDO ; QIU, XINKAI ; PORTALE, GIUSEPPE ; DONG, JINGJIN ; TALSMA, WYTSE ; YE, GANG ; SENGRIAN, APRIZAL AKBAR ; SOUZA, PAULO C. T. ; LOI, MARIA ANTONIETTA ; CHIECHI, RYAN C. ; MARRINK, SIEWERT J. ; HUMMELEN, JAN C. ; KOSTER, L. JAN ANTON . Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains. ADVANCED MATERIALS , v. -, p. 1704630, 2018.

• ZANOTTO, LEANDRO ; HEERDT, GABRIEL ; SOUZA, P. C. T. ; ARAUJO, GUIDO ; SKAF, M. S. . High performance collision cross section calculation-HPCCS. JOURNAL OF COMPUTATIONAL CHEMISTRY , v. 39, p. 1675-1681, 2018.

• MOTTIN, MELINA ; SOUZA, PAULO ; RICCI, CLARISSE ; SKAF, MUNIR . CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands. International Journal of Molecular Sciences (Online) , v. 18, p. 15, 2017.

• TOSE, LILIAN V. ; SANTOS, NAYARA A. ; RODRIGUES, RAYZA R.T. ; MURGU, MICHAEL ; GOMES, ALEXANDRE F. ; VASCONCELOS, GÉSSICA A. ; SOUZA, PAULO C.T. ; VAZ, BONIEK G. ; ROMÃO, WANDERSON . Isomeric separation of cannabinoids by UPLC combined with ionic mobility mass spectrometry (TWIM-MS)-Part I. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY , v. 418, p. 112-121, 2017.

• HSU, PIN-CHIA ; BRUININKS, BART M. H. ; JEFFERIES, DAMIEN ; CESAR TELLES DE SOUZA, PAULO ; LEE, JUMIN ; PATEL, DHILON S. ; MARRINK, SIEWERT J. ; QI, YIFEI ; KHALID, SYMA ; IM, WONPIL . CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. JOURNAL OF COMPUTATIONAL CHEMISTRY , v. 38, p. 2354-2363, 2017.

• SOUZA, P. C. T. ; TEXTOR, LARISSA C. ; MELO, DENISE C. ; NASCIMENTO, A. S. ; Skaf, Munir S. ; Polikarpov, Igor . An alternative conformation of ERbeta bound to estradiol reveals H12 in a stable antagonist position. Scientific Reports , v. 7, p. 3509, 2017.

• MOTTIN, M. ; SOUZA, P. C. T. ; RICCI, CLARISSE ; SKAF, MUNIR . CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , v. 18, p. 15, 2017.

• MOTTIN, MELINA ; SOUZA, PAULO C. T. ; SKAF, MUNIR S. . Molecular Recognition of PPARγ by Kinase Cdk5/p25: Insights from a Combination of Protein-Protein Docking and Adaptive Biasing Force Simulations. Journal of Physical Chemistry. B , v. 119, p. 8330-8339, 2015.

• SOUZA, P.C.T. ; PUHL, A.C. ; MARTÍNEZ, L. ; APARÍCIO, R ; NASCIMENTO, A.S. ; FIGUEIRA, A.C.M. ; NGUYEN, P. ; WEBB, P. ; SKAF, M.S ; POLIKARPOV, I. . Identification of a NEW HORMONE binding site ON THE SURFACE of thyroid hormone receptor. MOLECULAR ENDOCRINOLOGY , v. 28, p. me.2013-1359, 2014.

• BERNARDES, AMANDA ; SOUZA, PAULO C.T. ; MUNIZ, JOÃO R.C. ; RICCI, CLARISSE G. ; AYERS, STEPHEN D. ; PAREKH, NILI M. ; GODOY, ANDRÉ S. ; TRIVELLA, DANIELA B.B. ; REINACH, PETER ; WEBB, PAUL ; SKAF, MUNIR S. ; POLIKARPOV, IGOR . Molecular Mechanism of Peroxisome Proliferator-Activated Receptor α Activation by WY14643: a New Mode of Ligand Recognition and Receptor Stabilization. Journal of Molecular Biology , v. 425, p. 2878-2893, 2013.

• AMATO, A. A. ; RAJAGOPALAN, S. ; LIN, J. Z. ; CARVALHO, B. M. ; FIGUEIRA, A. C. M. ; LU, J. ; AYERS, S. D. ; MOTTIN, M. ; SILVEIRA, R. L. ; SOUZA, P. C. T. ; MOURAO, R. H. V. ; SAAD, M. J. A. ; TOGASHI, M. ; SIMEONI, L. A. ; ABDALLA, D. S. P. ; SKAF, M. S. ; POLIKPARPOV, I. ; LIMA, M. C. A. ; GALDINO, S. L. ; BRENNAN, R. G. ; et.al . GQ-16, a Novel Peroxisome Proliferator-activated Receptor   (PPAR ) Ligand, Promotes Insulin Sensitization without Weight Gain. JOURNAL OF BIOLOGICAL CHEMISTRY , v. 287, p. 28169-28179, 2012.

• LIBERATO, MARCELO VIZONÁ ; NASCIMENTO, ALESSANDRO S. ; AYERS, STEVEN D. ; LIN, JEAN Z. ; CVORO, ALEKSANDRA ; SILVEIRA, RODRIGO L. ; MARTÍNEZ, LEANDRO ; SOUZA, PAULO C. T. ; SAIDEMBERG, DANIEL ; DENG, TUO ; AMATO, ANGELA ANGELICA ; TOGASHI, MARIE ; HSUEH, WILLA A. ; PHILLIPS, KEVIN ; PALMA, MÁRIO SÉRGIO ; NEVES, FRANCISCO A. R. ; SKAF, MUNIR S. ; WEBB, PAUL ; POLIKARPOV, IGOR . Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan-PPAR Partial Agonists. PLoS One , v. 7, p. e36297, 2012.

• SOUZA, P. C. T. ; BARRA, G. B. ; VELASCO, L. F. R. ; RIBEIRO, I. C. J. ; SIMEONI, L. A. ; TOGASHI, M. ; WEBB, P. ; NEVES, F. A. R. ; SKAF, M. S. ; MARTÍNEZ, L. ; POLIKARPOV, I. . Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants. JOURNAL OF MOLECULAR BIOLOGY , v. 412, p. 882-893, 2011.

• PRATES, ÉRICA T. ; SOUZA, PAULO C. T. ; PICKHOLZ, MÓNICA ; SKAF, MUNIR S. . CHARMM-based parameterization of neutral articaine-A widely used local anesthetic. International Journal of Quantum Chemistry , v. 111, p. 1339-1345, 2011.

• HANSSON, ANDERS ; SOUZA, PAULO C. T. ; SILVEIRA, RODRIGO L. ; MARTÍNEZ, LEANDRO ; SKAF, MUNIR S. . CHARMM force field parameterization of rosiglitazone. International Journal of Quantum Chemistry , v. 111, p. 1346-1354, 2011.

• FIGUEIRA, A. C. M. ; SAIDEMBERG, D. M. ; SOUZA, P. C. T. ; MARTINEZ, L. ; SCANLAN, T. S. ; BAXTER, J. D. ; SKAF, M. S. ; PALMA, M. S. ; WEBB, P. ; POLIKARPOV, I. . Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange. MOLECULAR ENDOCRINOLOGY , v. 25, p. 15-31, 2010.

• MARTI'NEZ, LEANDRO ; SOUZA, PAULO C. T. ; GARCIA, WANIUS ; BATISTA, FERNANDA A. H. ; PORTUGAL, RODRIGO V. ; NASCIMENTO, ALESSANDRO S. ; NAKAHIRA, MARCEL ; LIMA, LUIS M. T. R. ; POLIKARPOV, IGOR ; SKAF, MUNIR S. . On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors. Journal of Physical Chemistry. B , v. 114, p. 1529-1540, 2010.

• ALESSANDRI, RICCARDO ; THALLMAIR, SEBASTIAN ; HERRERO, C. G. ; MERA-ADASME, RAÚL ; MARRINK, S. J. ; SOUZA, PAULO C.T. . A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations. In: Yong Wang, Ruhong Zhou. (Org.). A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules. 1ed.: AIP Publishing, 2023, v. , p. 11-134.

• SAMI, S. ; GRÜNEWALD, FABIAN ; SOUZA, P. C. T. ; MARRINK, S. J. . A Guide to Titratable Martini Simulations. In: Yong Wang, Ruhong Zhou. (Org.). A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules. 1ed.: AIP Publishing, 2023, v. , p. 41-416.

• GRÜNEWALD, FABIAN ; Kroon, Peter C. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . Protocol for Simulations of PEGylated Proteins with Martini 3. In: Chen Y.W., Yiu CP.B.. (Org.). Methods in Molecular Biology. 1sted.New York: Springer US, 2021, v. 2199, p. 315-335.

• HEERDT, GABRIEL ; ZANOTTO, LEANDRO ; SOUZA, PAULO C. T. ; ARAUJO, GUIDO ; Skaf, Munir S. . Collision Cross Section Calculations Using HPCCS. Methods in Molecular Biology. -ed.New York: Springer US, 2020, v. 2084, p. 297-310.

• BRUININKS, BART M. H. ; SOUZA, PAULO C. T. ; MARRINK, SIEWERT J. . A Practical View of the Martini Force Field. In: Bonomi M., Camilloni C.. (Org.). Methods in Molecular Biology. 1sted.New York: Springer New York, 2019, v. 2022, p. 105-127.

• BRANDNER, A. F. ; SOUZA, P. C. T. ; MARRINK, S. J. ; KHALID, SYMA . Toward a systematic modeling approach for coarse-grained carbohydrates. In: 68th Annual Meeting of the Biophysical Society, 2024, Philadelphia. Biophysical Journal, 2024. v. 123. p. 297A.

• GRÜNEWALD, FABIAN ; SOUZA, P. C. T. ; MARRINK, S. J. . The martini 3 ecosystem for coarse-grained simulations. In: 68th Annual Meeting of the Biophysical Society, 2023, San Diego. Biophysical Journal, 2023. v. 122. p. 419a-420a.

• SAHOO, AMITA R. ; SOUZA, PAULO C.T. ; MENG, Z. ; BUCK, MATTHIAS . How transmembrane helices of type 1 receptors transmit information: prediction of dimers with the Martini 3 coarse grained model. In: 66th Annual Meeting of the Biophysical Society, 2022, San Francisco. Biophysical Journal, 2022. v. 121. p. 464A.

• GRÜNEWALD, FABIAN ; SOUZA, PAULO C.T. ; MARRINK, S. J. . From peg to plasmid: system building for MD simulations of flexible macromolecules. In: 66th Annual Meeting of the Biophysical Society, 2022, San Francisco. Biophysical Journal, 2022. v. 121. p. 273A.

• PEREIRA, GILBERTO P. ; JANG, S. H. ; SIVAKUMAR, D. ; MUDEDLA, S. K. ; MARTIN, JULIETTE ; WU, SANGWOOK ; SOUZA, PAULO C.T. . Towards designing PROTACs by coarse-grained modeling. In: 17th Annual Drug Discovery Chemistry, 2022, San Diego. Abstract, 2022.

• JEFFERYS, E. E. ; BRUININKS, B. M. ; SOUZA, P.C.T. ; MARRINK, S. J. ; SANSOM, MARK S.P. . Towards Molecular Simulations of Juxtaposed Biomembranes. In: 63rd Annual Meeting of the Biophysical Society, 2019, Baltimore. Biophysical Journal, 2019. v. 116. p. 176A.

• BRUININKS, B. M. ; SOUZA, P. C. T. ; MARRINK, S. J. . Microscopic View on Non-viral Mediated Transfection. In: 62nd Annual Meeting of the Biophysical Society, 2018, San Francisco. Biophysical Journal. Maryland Heights: Cell Press, 2018. v. 114. p. p602a.

• SOUZA, P. C. T. ; WASSENAAR, T. A. ; SKAF, M. S. ; MARRINK, S. J. . TLR4 Recruitment into Lipid Rafts Studied by Coarse Grained MD Simulation. In: 62nd Annual Meeting of the Biophysical Society, 2018, San Francisco. Biophysical Journal. Maryland Heights: Cell Press, 2018. v. 114. p. p72a.

• HEERDT, G. ; ZANOTTO, L. N. ; SOUZA, P.C.T. ; ARAUJO, G. C. S. ; SKAF, M. S. . High performance collision cross section calculation-HPCCS. In: XIX Simpósio Brasileiro de Química Teórica, 2017, Águas de Lindóia. Trabalhos Apresentados, 2017.

• SOUZA, P.C.T. ; MARRINK, S.J. ; SKAF, M. S. . TLR4 recruitment into lipid rafts studied by coarse grained MD simulation. In: DutchBiophysics Meeting, 2016, Veldhoven. Abstract book, 2016.

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, M. S. . Influence of bacterial LPS and dietary fatty acids in the location of TLR4 in lipid rafts studied by coarse grained MD simulation. In: CECAM Workshop: Understanding function of proteins in membrane by atomistic and multiscale simulations, 2015, Lugano. Abstract Book, 2015.

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, MUNIR S. . Relationship between Obesity and TLR4-MD2 Receptors: New Studies by All-Atom and Coarse Grained MD Simulations. In: Congresso dei Chimici Teorici di Espressione Latina - CHITEL, 2015, Turim. Chitel BOOKLET, 2015.

• SOUZA, P. C. T. ; SKAF, M. S. . Relationship between Obesity and TLR4 Receptors: new studies by molecular dynamics simulations. In: I Workshop - CEPID Center for Computational Engineering & Sciences, 2014, Campinas. Abstracts of I Workshop - CEPID Center for Computational Engineering & Sciences. Campinas, 2014.

• MELO, D. C. ; SOUZA, P. C. T. ; SKAF, M. S. . Molecular basis for the relationship between ERα and ERβ. In: I Workshop - CEPID Center for Computational Engineering & Sciences, 2014, Campinas. Abstracts of I Workshop - CEPID Center for Computational Engineering & Sciences. Campinas, 2014.

• MOTTIN, M. ; SOUZA, P. C. T. ; SKAF, M. S. . Molecular Mechanisms of PPARγ phosphorylation by Cdk5: physical and chemical inhibition promoted by PPARγ ligands. In: I Workshop - CEPID Center for Computational Engineering & Sciences, 2014, Campinas. Abstracts of I Workshop - CEPID Center for Computational Engineering & Sciences. Campinas, 2014.

• SOUZA, P. C. T. ; SKAF, M.S . Relationship between Obesity and TLR4-MD2 Receptors: new studies by molecular dynamics simulations. In: BrazMedChem2014 - The 7th Brazilian Symposium on Medicinal Chemistry, 2014, Campos do Jordão. E-book of BrazMedChem2014, 2014. p. CAB-091.

• MOTTIN, M. ; SOUZA, P. C. T. ; SKAF, M.S . Modulation of PPARγ via phosphorylation: interactions between PPA0Rγ and a kinase enzyme. In: BrazMedChem2014 - The 7th Brazilian Symposium on Medicinal Chemistry, 2014, Campos do Jordão. E-book of BrazMedChem2014, 2014. p. CAB-010.

• SOUZA, P. C. T. ; TEXTOR, L. C. ; MELO, D. C. ; SKAF, M. S. ; POLIKARPOV, I. . Molecular basis for the 'Yin-Yang' relationship between ERalpha and ERbeta: An alternative conformation of ERbeta LBD bound to estradiol shows H12 in a stable antagonist position. In: Nuclear receptors: Linking molecules, genomes & physiology, 2013, Sorrento. Programme & Abstract Book, 2013. p. 129.

• SOUZA, P. C. T. ; PUHL, A. C. ; MARTÍNEZ, L. ; APARICIO, R. ; NASCIMENTO, A. S. ; FIGUEIRA, A. C. M. ; NGUYEN, P. ; WEBB, P. ; SKAF, M. S. ; POLIKARPOV, I. . Identification of a new hormone binding site on the surface of thyroid hormone receptor. In: Nuclear receptors: Linking molecules, genomes & physiology, 2013, Sorrento. Programme & Abstract Book, 2013. p. 133.

• MOTTIN, M. ; SOUZA, P. C. T. ; SILVEIRA, R. L. ; SKAF, M. S. . Molecular Dynamics Simulations of PPARγ with a new partial agonist FNB1. In: São Paulo School of Advanced Science (ESPCA): Advanced Topics in Computational Biology - Agrochemical and Drug Design, 2012, Campinas. Abstract Book ESPCA 2012, 2012.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Calculation of ΔGbinding of thyroid hormone to a new binding site of its receptor via the Jarzynski Equality and MD simulations. In: 8th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2012, Campinas. Abstract Book X-Meeting 2012, 2012.

• SOUZA, P. C. T. ; FIGUEIRA, A. C. M. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . New insights of Structure and Dynamics of the Thyroid Hormone Receptors without ligands. In: II Latin American Federation of Biophysical Societies Congress / XXXVII Brazilian Biophysical Society Congress, 2012, Búzios. Abstract Book LAFeBS 2012, 2012.

• MOTTIN, M. ; SOUZA, P. C. T. ; SILVEIRA, R. L. ; SKAF, M. S. . Studies of PPAR gamma receptor dynamics and its interaction with the new partial agonist GQ-16. In: 8th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2012, Campinas. Abstract Book X-Meeting 2012, 2012.

• MOTTIN, M. ; SOUZA, P. C. T. ; SILVEIRA, R. L. ; SKAF, M. S. . Molecular Dynamics simulation of the nuclear receptor PPAR gamma with a new partial agonist GQ-16. In: II Latin American Federation of Biophysical Societies Congress / XXXVII Congress of the Brazilian Biophysical Society, 2012, Búzios. Abstract Book LAFeBS 2012, 2012.

• MELO, D. C. ; SOUZA, P. C. T. ; SKAF, M. S. . Molecular Dynamics Simulations of Estrogen Receptors Mutations. In: II Latin American Federation of Biophysical Societies Congress / XXXVII Congress of the Brazilian Biophysical Society, 2012, Búzios. Abstract Book LAFeBS 2012, 2012.

• DA SILVA, J. C. A. ; SOUZA, P. C. T. ; SKAF, M. S. . Molecular Basis of Functional Impairment of Androgen Receptor Mutants Studied by Molecular Dynamics Simulations. In: XXXVIII Congresso de Químicos Teóricos de Expressão Latina (Quitel), 2012, Natal. Abstract Book Quitel 2012, 2012.

• RAJAGOPALAN, S. ; AMATO, A. A. ; CARVALHO, B. M. ; FIGUEIRA, A. C. M. ; AYERS, S. D. ; MOTTIN, M. ; SILVEIRA, R. L. ; SOUZA, P. C. T. ; MOURAO, R. H. ; SAAD, M. J. A. ; TOGASHI, M. ; SIMEONI, L. A. ; ABDALLA, D. S. P. ; SKAF, M. S. ; POLIKARPOV, I. ; LIMA, M. C. A. ; GALDINO, S. L. ; BRENNAN, R. G. ; BAXTER, J. D. ; PITTA, I. R. ; et.al . Structural Basis of Idealized Selective PPARγ Modulation. In: The Endocrine Society's 94th Annual Meeting and Expo, 2012, Houston. Endocrine Reviews - Meeting Abstracts: Glucose Homeostasis: Integrative & Endocrine Metabolic Control, 2012. v. 33. p. OR10-4.

• GOZZO, F. C. ; GOMES, A. F. ; SOUZA, P. C. T. ; SKAF, M. S. . Effect of Chemical Cross-Linking on Protein Structure Investigated by Travelling-Wave Ion Mobility Mass Spectrometry and Molecular Dynamics Simulations. In: 59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011, Denver, Colorado. Proceedings of the 59th ASMS Conference on Mass Spectrometry and Allied Topics, 2011.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Studies of thyroid hormone receptor and its mutations. In: São Paulo School of Advanced Science on Natural Products, Medicinal Chemistry and Organic Synthesis, 2011, Campinas. Abstract Book, 2011.

• MOTTIN, M. ; SOUZA, P. C. T. ; SILVEIRA, R. L. ; SKAF, M. S. . Investigation of a new PPARgamma partial agonist by Molecular Dynamics Simulations. In: 7th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2011, Florianópolis. Abstract Book X-Meeting 2011, 2011.

• DA SILVA, J. C. A. ; SOUZA, P. C. T. ; SKAF, M. S. . Molecular Dynamics Simulations of the Androgen Receptor LBD: Molecular Basis of Structure-Function Relationship. In: 7th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2011, Florianópolis. Abstract Book, 2011.

• SOUZA, P. C. T. ; FIGUEIRA, A. C. M. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . New insights of Structure and Dynamics of the Thyroid Hormone Receptors without ligands. In: 7th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2011, Florianópolis. Abstract Book, 2011.

• SOUZA, P. C. T. ; POLIKARPOV, I. ; MARTÍNEZ, L. ; SKAF, M. S. . Calculation of ΔGbinding of thyroid hormone to a new binding site of its receptor via the Jarzynski Equality and MD simulations. In: XVI Simpósio Brasileiro de Química Teórica, 2011, Ouro Preto. Livro de Resumos. Belo Horizonte: Editora UFOP, 2011.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Studies of thyroid hormone receptor and its mutations. In: 33ª Reunião Anual da Sociedade Brasileira de Química, 2010, Águas de Lindóia. CD com o Programa Completo - Lista de Resumos, 2010.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Studies of thyroid hormone receptor and its mutations. In: 3rd Latin American Protein Society Meeting, 2010, Salta. Abstract book, 2010. p. 293-293.

• FIGUEIREDO, A. R. ; SOUZA, P. C. T. ; SKAF, M. S. ; GOZZO, F. C. . Evaluation of Cross-linker and Protein Dynamics in Cross-linking Coupled to Mass Spectrometry Experiments. In: 3rd Latin American Protein Society Meeting, 2010, Salta. Abstract book, 2010. p. 296-296.

• FIGUEIREDO, A. R. ; SOUZA, P. C. T. ; SKAF, M. S. ; GOZZO, F. C. . Evaluation of Cross-linker and Protein Dynamics in Cross-linking Coupled to Mass Spectrometry Experiments. In: 57th ASMS Conference on Mass Spectrometry and Allied Topics, 2009, Philadelphia, Pennsylvania. Proceedings of the 57th ASMS Conference on Mass Spectrometry, 2009.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; BARRA, G. B. ; NEVES, F. A. R. ; POLIKARPOV, I. ; SKAF, M. S. . A Importância Funcional de Mutações no Resíduo I280 para a Atividade do Receptor do Hormônio Tireoideano: Dinâmiica Molecular elucida Ensaios Funcionais. In: XV Simpósio Brasileiro de Química Teórica, 2009, Poços de Caldas - MG. Livro de resumos, 2009. p. 196.

• FIGUEIREDO, A. R. ; SOUZA, P. C. T. ; SKAF, M. S. ; GOZZO, F. C. . Evaluation of Cross-linker and Protein Dynamics in Cross-linking Coupled to Mass Spectrometry Experiments.. In: 3º. Congresso Brasileiro de Espectrometria de Massas (BrMASS 2009), 2009, Campinas. Livro de Resumos, 2009.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Study of thyroid hormone receptor and its mutations. In: X-meeitng - 4th International Conference of the Brazilian Association for Bioinformatics and Computational Biology, 2008, Salvador. X-meeitng - Abstracts - CD-ROM, 2008.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Molecular Dynamics show changes in structure, mobility and interactions of nuclear receptor mutants related with syndrome. In: BrazMedChem2008 - The 4th Brazilian Symposium on Medicinal Chemistry, 2008, Ipojuca - Porto de Galinhas. BrazMedChem2008 - The 4th Brazilian Symposium on Medicinal Chemistry - CDROM, 2008.

• HANSSON, A. O. ; SOUZA, P. C. T. ; POLIKARPOV, I. ; SKAF, M. S. . Molecular Properties of the Nuclear Receptor Ligand Rosiglitazone. In: BrazMedChem2008 - The 4th Brazilian Symposium on Medicinal Chemistry, 2008, Ipojuca - Porto de Galinhas. BrazMedChem2008 - The 4th Brazilian Symposium on Medicinal Chemistry - CDROM, 2008.

• SOUZA, P. C. T. ; SKAF, M. S. . Dinâmica Molecular mostra mudanças de mobilidade na estrutura de Receptores Nucleares relacionados a Síndrome. In: XV Congresso de Iniciação Científica da UNICAMP, 2007, Campinas. Caderno de Resumos do XV Congresso Interno de Iniciação Científica, 2007.

• MARTÍNEZ, L. ; SOUZA, P. C. T. ; POLIKARPOV, I. ; SKAF, M. S. . Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors. In: X-Meeting, 3rd International conference of the Brazilian Association for Bioinformatics and Computational Biology, 2007, São Paulo. Proceedings: CD-ROM, 2007. p. 137-137.

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Study of Thyroid Hormone Receptor Dynamics and its Mutations. In: XIV Simpósio Brasileiro de Química Teórica, 2007, Poços de Caldas. Resumos, 2007.

• MARTÍNEZ, L. ; SOUZA, P. C. T. ; POLIKARPOV, I. ; SKAF, M. S. . Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors. In: XIV Simpósio Brasileiro de Química Teórica, 2007, Poços de Caldas. Resumos, 2007.

• SOUZA, P. C. T. ; SKAF, M. S. . Introdução a Dinâmica Molecular de Proteínas. In: XIV Congresso de Iniciação Científica da UNICAMP, 2006, Campinas. Caderno de resumos do XIV Congresso Interno de Iniciação Científica, 2006.

• SOUZA, P.C.T. . Invited Lecture: On the road to molecular design with the Martini coarse-grained model - University of Montpellier. 2024. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. . Oral Presentationl: On the road to molecular design with the Martini coarse-grained model - Summer Workshop in Computational Chemistry. 2024. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. . Oral presentation: Enhancing drug design using the Martini Coarse-Grained Model - ALLODD ? 3rd Training School & Networking Meeting. 2024. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. . Oral presentation: Martini coarse-grained model: from beads to complex interfaces. 2024. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Invited Lecture: On the road to biomolecular design with the Martini coarse-grained model - Frankfurt Institute for Advanced Studies. 2023. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Invited Lecture: On the road to biomolecular design with the Martini coarse-grained model - Forschungszentrum Jülich GmbH. 2023. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Invited Lecture: On the road to molecular design with the Martini coarse-grained model - Institut Lumière Matière, Université Claude Bernard Lyon 1. 2023. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. . Oral presentation: On the road to biomolecular design with the Martini coarse-grained model - The 10th Anniversary Symposium of the Center for Multiscale Theory and Computation. 2023. (Apresentação de Trabalho/Simpósio).

• SOUZA, PAULO C.T. . Oral presentation: Martini 3 Coarse-Grained Model: from better beads to a broader scope - Lecture series in Molecular Modelling, PomaLab. 2022. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Oral presentation: Computational microscopy of membrane proteins with Martini 3 models. - Inserm Workshop. 2022. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Poster: Towards designing PROTACs by coarse-grained modeling - Drug Discovery Chemistry event. 2022. (Apresentação de Trabalho/Congresso).

• SOUZA, PAULO C.T. . Oral presentation: MARTINI 3: A General Purpose Coarse-grained Force Field - ACS Spring Meeting 2021. 2021. (Apresentação de Trabalho/Congresso).

• SOUZA, PAULO C.T. . Oral presentation: Biomolecular Design with Martini Model: From Small-molecules to Lipid Nanoparticles - Multiscale Modeling for Biotherapeutics, BITC and Schrödinger. 2021. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. . Oral presentation: Introduction to Martini 3 - Martini online workshop. 2021. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. . Oral presentation: Drug Design with Martini 3 Coarse-Grained Model - 22th GGMM and 10th SFCi meetings. 2021. (Apresentação de Trabalho/Congresso).

• SOUZA, P. C. T. . Oral presentation: Protein-small molecule binding with Martini 3 - Martini online workshop. 2021. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C.T. . Oral presentation: MARTINI 3: A General Purpose Coarse-grained Force Field - ACS Spring. 2020. (Apresentação de Trabalho/Congresso).

• SOUZA, P.C.T. . Oral presentation: MARTINI 3 : A General Purpose Coarse-grained Force Field - 1st Martini Retreat. 2019. (Apresentação de Trabalho/Outra).

• SOUZA, P.C.T. ; WASSENAAR, TSJERK A. ; SKAF, M. S. ; MARRINK, S. J. . Poster:TLR4 Recruitment into Lipid Rafts Studied by Coarse Grained MD Simulation - 62nd Annual Meeting of the Biophysical Society. 2018. (Apresentação de Trabalho/Congresso).

• SOUZA, P.C.T. . Oral presentation: The future prospects of the MARTINI Force Field - Cecam workshop. 2018. (Apresentação de Trabalho/Outra).

• SOUZA, PAULO C. T. . Oral presentation: Future of Martini Force Field - Martini Workshop. 2017. (Apresentação de Trabalho/Outra).

• SOUZA, P.C.T. ; MARRINK, S.J. ; SKAF, M. S. . Poster: TLR4 recruitment into lipid rafts studied by coarse grained MD simulation - Dutch Biophysics Meeting. 2016. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, M.S . Poster: Relationship between Obesity and TLR4-MD2 Receptors: New Studies by All-Atom and Coarse Grained MD Simulations. 2015. (Apresentação de Trabalho/Congresso).

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, M. S. . Oral presentation/Poster: Influence of bacterial LPS and dietary fatty acids in the location of TLR4 in lipid rafts studied by coarse grained MD simulation. 2015. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, MUNIR S. . Oral presentation: Molecular mechanisms of Fatty Acid binding to TLR4: New Studies by AA and CG MD Simulations - 25th Intl. BIOMOS Symposium on Biomolecular Simulation. 2015. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, M. S. . Poster: Relationship between Obesity and TLR4-MD2 Receptors: New Studies by All-Atom and Coarse Grained MD Simulations. 2015. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; MARRINK, S. J. ; SKAF, M. S. . Oral presentation: Molecular mechanisms of Fatty Acid binding to TLR4: New Studies by AA and CG MD Simulations. 2015. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; SKAF, M. S. . Poster: Relationship between Obesity and TLR4 Receptors: new studies by molecular dynamics simulations. 2014. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; SKAF, M.S . Poster: In silico modelling of disease-related mutations in proteins: aplication to nuclear receptors and toll-like receptors. 2014. (Apresentação de Trabalho/Conferência ou palestra).

• SOUZA, P. C. T. ; SKAF, MUNIR S. . Poster: Relationship between Obesity and TLR4-MD2 Receptors: new studies by molecular dynamics simulations. 2014. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; PUHL, A. C. ; MARTINEZ, L. ; APARICIO, R. ; NASCIMENTO, A. S. ; FIGUEIRA, A. C. M. ; NGUYEN, P. ; WEBB, P. ; SKAF, M. S. ; POLIKARPOV, I. . Poster: Identification of a new hormone binding site on the surface of thyroid hormone receptor. 2013. (Apresentação de Trabalho/Congresso).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Calculation of ΔGbinding of thyroid hormone to a new binding site of its receptor via the Jarzynski Equality and MD simulations. 2012. (Apresentação de Trabalho/Conferência ou palestra).

• SOUZA, P. C. T. ; FIGUEIRA, A. C. M. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: New insights of Structure and Dynamics of the Thyroid Hormone Receptors without ligands. In: 7th Internacional Conference of the Brazilian Association for Bioinformatics and Computational Biology. 2012. (Apresentação de Trabalho/Congresso).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Studies of thyroid hormone receptor and its mutations. 2011. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; FIGUEIRA, A. C. M. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: New insights of Structure and Dynamics of the Thyroid Hormone Receptors without ligands. 2011. (Apresentação de Trabalho/Conferência ou palestra).

• SOUZA, P. C. T. ; POLIKARPOV, I. ; MARTÍNEZ, L. ; SKAF, M. S. . Poster: Calculation of ΔGbinding of thyroid hormone to a new binding site of its receptor via the Jarzynski Equality and MD simulations. 2011. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Studies of thyroid hormone receptor and its mutations. 2010. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Studies of thyroid hormone receptor and its mutations. 2010. (Apresentação de Trabalho/Outra).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; BARRA, G. B. ; NEVES, F. A. R. ; POLIKARPOV, I. ; SKAF, M. S. . Oral presentation/Poster: A Importância Funcional de Mutações no Resíduo I280 para a Atividade do Receptor do Hormônio Tireoideano: Dinâmica Molecular elucida Ensaios Funcionais. 2009. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Study of thyroid hormone receptor and its mutations - 4th X-meeitng. 2008. (Apresentação de Trabalho/Conferência ou palestra).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Molecular Dynamics show changes in structure, mobility and interactions of nuclear receptor mutants related with syndrome. 2008. (Apresentação de Trabalho/Simpósio).

• MARTÍNEZ, L. ; SOUZA, P. C. T. ; POLIKARPOV, I. ; SKAF, M. S. . Oral presentation: Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors. 2007. (Apresentação de Trabalho/Conferência ou palestra).

• SOUZA, P. C. T. ; MARTÍNEZ, L. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Study of Thyroid Hormone Receptor Dynamics and its Mutations - XIV Simpósio Brasileiro de Química Teórica. 2007. (Apresentação de Trabalho/Simpósio).

• MARTÍNEZ, L. ; SOUZA, P. C. T. ; POLIKARPOV, I. ; SKAF, M. S. . Poster: Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors - XIV Simpósio Brasileiro de Química Teórica. 2007. (Apresentação de Trabalho/Simpósio).

• SOUZA, P. C. T. ; SKAF, M. S. . Poster: Dinâmica Molecular mostra mudanças de mobilidade na estrutura de Receptores Nucleares relacionados a Síndrome - XV Congresso de Iniciação Científica da UNICAMP. 2007. (Apresentação de Trabalho/Congresso).

• SOUZA, P. C. T. ; SKAF, M. S. . Poster: Introdução a Dinâmica Molecular de Proteínas - XIV Congresso de Iniciação Científica da UNICAMP. 2006. (Apresentação de Trabalho/Congresso).

• Kroon, Peter C. ; GRÜNEWALD, FABIAN ; BARNOUD, JONATHAN ; TILBURG, M. V. ; SOUZA, P.C.T. ; WASSENAAR, TSJERK A. ; MARRINK, SIEWERT J . Martinize2 and Vermouth: Unified Framework for Topology Generation. eLife, 2024 (Preprint).

Outras produções

Projetos de pesquisa

• 2021 - Atual

  Coarse-Grained modeling of ABC transporters: conformation dynamics and applications to antimicrobials, Descrição: Bacterial resistance is a serious worldwide problem and the need for new treatments is urgent. Creating new antibiotics demands the development of innovative drug discovery strategies applied to challenging new targets, as ABC transporters. These dynamic transmembrane proteins are molecular pumps that translocate a huge variety of molecules across the cell membrane. A growing number of evidences support the idea that these transporters are involved in antimicrobial resistance as they could confer to bacteria the ability to evade most of current therapies. The main goal of this proposal is to apply coarse-grained molecular dynamic simulations to study two problems related with ABC transporters and antibiotic resistance: (i) study the conformational dynamics of BmrA, a multidrug efflux transporter; (ii) finding the binding pockets and the action mechanism of new ECF transporter inhibitors. Both problems demand intensive computational resources and new developments of the Martini 3 force field. The new methodological approaches and its application to ABC transporters will allow screening of drugs applied to difficult targets, including flexible transmembrane proteins ? which is currently not feasible with any available method.. , Situação: Em andamento; Natureza: Pesquisa. , Integrantes: Paulo Cesar Telles de Souza - Coordenador.

• 2021 - Atual

  Coarse-Grained modeling applied to virtual drug design of PROTACs and to Lipid Nanoparticles for RNA delivery, Descrição: Here we propose to use this CG force-field as based to develop innovative virtual screening protocols for two important pharmaceutical problems: (i) development of new proteolysis targeting chimeras (PROTACs) drugs; (ii) development of lipid nanoparticle delivery systems for biopharmaceuticals as mRNA, as currently used in vaccines against SARS‐CoV. Both projects involve the use of the coarse-grained methodology already developed by the French partner, and the development of new methodology, namely force field parameters for new potential lead compounds and delivery systems, generated by novel virtual screening approaches based on the Martini coarse-grained model. Both projects would be executed by two postdoc-fellows and one engineer in the host lab in France, with funding coming from the South Korea collaborator.. , Situação: Em andamento; Natureza: Pesquisa. , Integrantes: Paulo Cesar Telles de Souza - Coordenador / WU, SANGWOOK - Integrante / MONTICELLI, LUCA - Integrante.

• 2014 - 2015

  Simulações de dinâmica molecular coarse-graining de complexos de TLR4, Descrição: http://www.bv.fapesp.br/pt/bolsas/155117/simulacoes-de-dinamica-molecular-coarse-graining-de-complexos-de-tlr4/. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Paulo Cesar Telles de Souza - Integrante / SKAF, M.S - Coordenador / Siewert-Jan Marrink - Integrante.

• 2013 - 2016

  Relações entre a obesidade e o receptor TLR4: Novos estudos através de simulações de dinâmica molecular, Projeto certificado pelo(a) coordenador(a) Munir Salomao Skaf em 15/03/2013., Descrição: http://www.bv.fapesp.br/pt/bolsas/142930/relacoes-entre-a-obesidade-e-o-receptor-tlr4-novos-estudos-atraves-de-simulacoes-de-dinamica-molecul/. , Situação: Concluído; Natureza: Pesquisa. , Integrantes: Paulo Cesar Telles de Souza - Integrante / Lício Augusto Velloso - Integrante / SKAF, M.S - Coordenador.

• 2009 - 2013

  Simulações de Dinâmica Molecular de Receptores Nucleares: Estimativas de Energia Livre Ligante-Proteína, Descrição: http://www.bv.fapesp.br/pt/bolsas/112506/simulacoes-de-dinamica-molecular-de-receptores-nucleares-estimativas-de-energia-livre-ligante-protei/. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Doutorado: (1) . , Integrantes: Paulo Cesar Telles de Souza - Integrante / Munir Salomão Skaf - Coordenador., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa., Número de produções C, T & A: 11

• 2007 - 2009

  Simulações de Dinâmica Molecular de Mutantes do Receptor Nuclear do Hormônio Tireoideano, Descrição: http://www.bv.fapesp.br/pt/bolsas/106931/simulacoes-de-dinamica-molecular-de-mutantes-do-receptor-nuclear-do-hormonio-tireoideano/. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Mestrado acadêmico: (1) . , Integrantes: Paulo Cesar Telles de Souza - Integrante / Munir Salomão Skaf - Coordenador., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa., Número de produções C, T & A: 17

• 2005 - 2007

  Introdução a Dinâmica Molecular de Proteínas: Estudo da Mobilidade do Receptor Nuclear do Hormônio Tireoidiano e de mutantes, Descrição: http://www.bv.fapesp.br/pt/bolsas/58307/introducao-a-dinamica-molecular-de-proteinas/. , Situação: Concluído; Natureza: Pesquisa. , Alunos envolvidos: Graduação: (1) . , Integrantes: Paulo Cesar Telles de Souza - Integrante / Munir Salomão Skaf - Coordenador., Financiador(es): Fundação de Amparo à Pesquisa do Estado de São Paulo - Bolsa., Número de produções C, T & A: 4

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