Martínez Molecular Modeling Group

Institute of Chemistry and Center for Computing in Engineering and Science

University of Campinas

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Solvation structure and thermodynamics in complex solutions

    		• V. Piccoli, L. Martínez, Competitive Effects of Anions on Protein Solvation by Aqueous Ionic Liquids J. Phys. Chem. B, 2024. [Full Text]
    		• A. F. Pereira, L. Martínez, Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. J. Chem. Inf. Model. 68, 8, 3350-3359, 2024. [Full Text] [PDF] [Supporting Information]
    		• A. F. Pereira, V. Piccoli, L. Martínez, Trifluoroethanol direct interactions with protein backbones destabilize alpha-helices. J. Mol. Liq. 365 (2022) 120209. [Full Text] [PDF]
    		• V. Piccoli, L. Martínez, Ionic liquid solvation of proteins in native and denatured states. J. Mol. Liq. 363 (2022) 119953. [Full Text] [PDF]
    		• L. Martínez, ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective. J. Mol. Liq. 347, 117945, 2022. [Full Text] [PDF] [Associated Software]
    		• V. Piccoli, L. Martínez, Correlated counterion effects on the solvation of proteins by ionic liquids. J. Mol. Liq. 320, 114347, 2020. [Full Text] [PDF]
    		• I. P. de Oliveira, L. Martínez, The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation. Phys. Chem. Chem. Phys. 22, 354-367, 2020. [LINK] [PDF]
    		• L. Martínez, S. Shimizu, Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions. J. Chem. Theor. Comp. 13, 6358–6372, 2017 [LINK] [PDF] [Associated software] [Additional discussion]
    		• I. P. de Oliveira, L. Martínez, Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea. Phys. Chem. Chem. Phys. 18, 21797-21808, 2016. [PDF]
    		• R. L. Silveira, J. Martínez, M. S. Skaf, L. Martínez, Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide. J. Phys. Chem. B, 116, 5671-5678, 2012. [PDF]
    		• L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff. Computer Phys. Commun. 279, 108452, 2022. [Full Text] [PDF] [Associated Software]
    		• L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez, Packmol: A package for building initial configurations for molecular dynamics simulations, J. Comp. Chem. 30, 2157, 2009. [PDF] Associated software: [LINK]


    Protein structure modeling

    		• P. C. C. da Silva, L. Martínez, Extended Conformational Selection in the Antigen–Antibody Interaction of the PfAMA1 Protein. J. Phys. Chem. B, 2024. [Full Text]
    		• P. C. C. da Silva, L. Martínez, Intrinsically Disordered Malaria Antigens: An Overview of Structures, Dynamics and Molecular Simulation Opportunities. J. Braz. Chem. Soc. 35, 10, e-20240102, 1-21, 2024. [Full Text]
    		• G. F. Bottino, A. J. R. Ferrari, F. C. Gozzo, L. Martínez, Structural discrimination analysis for constraint selection in protein modeling. Bioinformatics, 21(37), 3766-3773, 2021. [Full Text] [PDF] [Associated Software]
    		• R. N. Santos, G. F. Bottino, F. C. Gozzo, F. Morcos, L. Martínez, Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution. Proteins, 88(4), 625-632, 2020. [Full Text] [PDF]
    		• A. J. R. Ferrari, F. C. Gozzo, L. Martínez, Statistical force-field for structural modeling using chemical cross-linking/mass-spectrometry distance constraints. Bioinformatics, 35(17), 3005-3012, 2019. [Full Text] [XLFF site]
    		• A. J. R. Ferrari, M. A. Clasen, L. Kurt, P. C. Carvalho, F. C. Gozzo, L. Martínez, TopoLink: Evaluation of structural models using chemical crosslinking distance constraints. Bioinformatics, 35(17), 3169-3170, 2019. [Full Text] [TopoLink site]
    		• R. N. Santos, X. Jiang, L. Martínez, F. Morcos, Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations. In: Computational Methods in Protein Evolution, Methods in Molecular Biology. vol. 1851. Springer 2019. [LINK]
    		• L. Censoni, L. Martínez, Prediction of kinetics of protein folding with non-redundant contact information. Bioinformatics, 34(23), 4034-4038, 2018. [LINK] [Associated software]
    		• R. N. dos Santos, A. J. R. Ferrari, H. C. R. de Jesus, F. C. Gozzo, F. Morcos, L. Martínez, Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics, 34(13), 2201-2208, 2018 [LINK] [Associated software]
    		• N. Duclert-Savatier, L. Martínez, M. Nilges, T. E. Malliavin, The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations. BMC Struct. Biol. 11:46, 2011. [LINK] [Associated Software]


    Molecular modeling methods and software

    Packmol
    		• L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez, Packmol: A package for building initial configurations for molecular dynamics simulations, J. Comp. Chem. 30, 2157, 2009. [PDF] Associated software: [LINK]
    		• J. M. Martínez, L. Martínez, Packing Optimization for Automated Generation of Complex System's Initial Configurations for Molecular Dynamics and Docking, J. Comp. Chem. 24, 819-825, 2003. [PDF] Associated software: [LINK]
    		• M. Soñora, L. Martínez, S. Pantano, M. R. Machado, Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. J. Chem. Inf. Model. 61(1), 408-422, 2021. [Full Text]
    		• L. Martínez, CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff Computer Phys. Commun. 279, 108452, 2022. [Full Text] [PDF] [Associated Software]

    Structural alignment
    		• L. Martínez, Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS ONE 10 (3): e01109264, 2015. [LINK] [Software]
    		• R. Andreani, J. M. Martínez, L. Martínez, F. Yano, Low Order Value Optimization and Applications, J. Glob. Optim. 43, 1-22, 2008. [PDF] Software associated to this article: MDLovoFit , LovoAlign, LovoFit
    		• R. Andreani, J. M. Martínez, L. Martínez, Trust-region superposition methods for protein alignment, IMA J. Numer. Anal. 28, 690-710, 2008. [PDF]
    		• R. Andreani, J. M. Martínez, L. Martínez, F. Yano, Continuous Optimization Methods for Structure Alignment, Math. Program. Ser. B. 112, 93-124, 2008. [PDF]
    		• L. Martínez, R. Andreani, J. M. Martínez, Convergent Algorithms for Protein Structural Alignment, BMC Bioinformatics, 8, 306, 2007. [PDF] Associated software: [LINK]

    Electronic structure calculation algorithms
    		• E. G. Birgin, J. M. Martínez, L. Martínez, G. B. Rocha, Sparse projected-gradient method as a linear-scaling low-memory alternative to diagonalization in self-consistent field electronic structure calculations. J. Chem. Theor. Comput. 9(2), 1043-1051, 2013. [PDF]
    		• J. B. Francisco, J. M. Martínez, L. Martínez, F. Pisnitchenko, Inexact Restoration method for minimization problems arising in electronic structure calculations, Comp. Optimiz. Appl. 50, 555-590, 2011. [PDF]
    		• J. B. Francisco, J. M. Martínez, L. Martínez, Density-based globally convergent trust-region methods for self-consistent field electronic structure calculations, J. Math. Chem. 40, 349-377, 2006. [PDF]
    		• J. B. Francisco, J. M. Martínez, L. Martínez, Globally convergent trust-region methods for self-consistent field electronic structure calculations, J. Chem. Phys. 121, 10863-10878, 2004. [PDF]


    Biomolecular spectroscopy

    		•  A. J. Lopez, E. P. Barros, L. Martínez, On the interpretation of subtilisin Carlsberg time-resolved fluorescence anisotropy decays: modeling with classical simulations. J. Chem. Inf. Model. 60 (2) 747-755, 2020. [Full Text]
    		• A. J. Lopez, L. Martínez, Parametric Models to Compute Tryptophan Fluorescence Wavelengths from Classical Protein Simulations. J. Comp. Chem. 39(19), 1249-1258, 2018 [Full Text] [LINK]
    		• M. R. B. Batista, L. Martínez, Dynamics of Nuclear Receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays. Biophys. J. 105(7), 1670-1680, 2013. [PDF] [Supplementary Data] [Associated Software]


    Education

    		• L. Martínez, Measuring the conductivity of very dilute electrolyte solutions, drop by drop. Química Nova, 41, 7, 814-817, 2018 [LINK] [Supplementary Information]
    		• L. Martínez, O Espectro Roto-Vibracional do Ácido Clorídrico, em "Química em 50 ensaios". L. Tasić (org.) Grupo Átomo e Alínea, 2017. [LINK]
    		• L. Martínez, Introducing the Levinthal's protein folding paradox and its solution. J. Chem. Educ. 91, 1918-1923, 2014. [PDF]
    		• L. Martínez, I. A. Borin, M. S. Skaf,, Fundamentos de Simulação por Dinâmica Molecular, em "Métodos de Química Teórica e Modelagem Molecular". Eds. N. H. Morgon e K. Coutinho, Editora Livraria da Física, São Paulo, 2007.


    Applications of modeling and simulations

    		• P. C. C. da Silva, L. Martínez, Intrinsically Disordered Malaria Antigens: An Overview of Structures, Dynamics and Molecular Simulation Opportunities J. Braz. Chem. Soc. 35, 10, e-20240102, 1-21, 2024. [Full Text]
    		• D. Bustos, M. Bedoya, D. Ramirez, G. Concha, L. Zuñiga, N. Decher, E. W. Hernández-Rodriguez, F. V. Sepúlveda, L. Martínez, W. González, Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K2P Channels. Int. J. Mol. Sci. 21(2), 532, 2020. [Full Text]
    		• T. H. Siqueira, L. Martínez, Molecular simulations of fluconazole-mediated inhibition of sterol biosynthesis. J. Biomol. Struct. Dyn. 38 (6) 1659-1669, 2020. [Full Text]
    		• L. Campos, P. Zenatti, L. Pissinato, G. Rodrigues, L. L. Artico, T. Guimarães, L. Archangelo, L. Martínez, A. Brooks, J. A. Yunes, Oncogenic basic amino acid insertions at the extracellular juxtamembrane region of IL7Ra cause receptor hypersensitivity. Blood, 133, 1259-1263, 2019. [LINK]
    		• I. P. de Oliveira, G. E. Jara, L. Martínez, Molecular mechanism of activation of Burkholderia cepacia Lipase at aqueous-organic interfaces. Phys. Chem. Chem. Phys. 19, 31499-31507, 2017 [LINK]
    		• L. Censoni, H. S. Muniz, L. Martínez, A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics, 33, 2106-2113, 2017. [LINK] [PDF] [Associated software]
    		• G. E. Jara, L. Martínez, Anthrax Edema Factor: An Ion-Adaptive Mechanism of Catalysis with Increased Transition State Conformational Flexibility. J. Phys. Chem. B, 120 (27), 6504-6514, 2016. [PDF] [Supplementary Information]
    		• L. H. F. Lima, V. I. Serpa, F. R. Rosseto, G. R. Sartori, M. O. Neto, L. Martínez, I. Polikarpov, Small-Angle X-ray Scattering and Structural Modeling of Full-Length Cellobiohydrolase I from Trichoderma harzianum. Cellulose 20(4), 1573-1585, 2013. [PDF]
    		• E. Laine, L. Martínez, D. Ladant, T. E. Malliavin, A. Blondel, Molecular Motions as a Drug Target: Mechanistic Simulations of Anthrax Toxin Edema Factor Function Led to the Discovery of Novel Allosteric Inhibitors. Toxins, 4(8), 580-604, 2012. [LINK]
    		• S. E. D. C. Jorge, A. A. Petruk, E. M. Kimura, D. M. Oliveira, L. Caire, C. N. Sueamasu, P. A. A. Silveira, D. M. Albuquerque, F. F. Costa, M. S. Skaf, L. Martínez, M. F. Sonati, Hb S-São Paulo: a new sickling hemoglobin with stable polymers and decreased oxygen affinity. Arch. Biochem. Biophys, 519, 23-31, 2012. [PDF]
    		• L. Martínez, T. E. Malliavin, A. Blondel, Mechanism of reactant and product dissociation from the Anthrax Edema Factor: a Locally Enhanced Sampling and Steered Molecular Dynamics Study, Proteins, 79, 1649-1661, 2011. [PDF] [Supplementary Information]
    		• A. Hansson, P. C. T. Souza, R. L. Silveira, L. Martínez, M. S. Skaf, CHARMM Force Field Parameterization of Rosiglitazone, Int. J. Quantum. Chem. 111, 1346-1354, 2011. [PDF]
    		• J. M. C. Mondego, M. P. Duarte, E. Kiyota, L. Martínez, S. R. Camargo, F. P. Caroli, B. S. C. Alves, S. M. C. Guerreiro, M. L. Oliva, O. Guerreiro-Filho, M. Menossi, Molecular characterization of a miraculin-like gene differentially expressed during coffee development and coffee leaf miner infestation, Planta, 233, 123-137, 2011. [PDF]
    		• L. Bleicher, E. Prates, T. Gomes, R. L. Silveira, A. S. Nascimento, A. Rojas, A. Golubev, L. Martínez, Munir S. Skaf, I. Polikarpov, Molecular basis for the thermostability and thermophilicity of laminarinases: X-ray structure of the hypherthermostable laminarinase from Rhodothermus marinus and molecular dynamics simulations. J. Phys. Chem. B, 115, 7940-7949, 2011. [PDF]
    		• E. Laine, L. Martínez, A. Blondel, T. E. Malliavin, Activation of the edema factor of Bacillus anthracis by calmodulin: Evidence of an interplay between the EF-calmodulin interaction and calcium binding, Biophys. J. 99, 2264-2272, 2010. [PDF]
    		• L. Martínez, E. Laine, T. E. Malliavin, M. Nilges, A. Blondel, ATP conformation and ion binding modes in the active site of the Anthrax Edema Factor: A computational analysis, Proteins 77, 971, 2009. [PDF]
    		• M. T. Sonoda, N. H. Moreira, L. Martínez, F. W. Favero, S. M. Vechi, L. R. Martins, M. S. Skaf, A review on the dynamics of water, Braz. J. Phys. 34, 3-15, 2004. [PDF]


    Nuclear Hormone Receptors

    		• M. R. B. Batista, L. Martínez, Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPARγ and Functional Implications. J. Phys. Chem. B, 119 (50), 15418-15429, 2015. [PDF]
    		• P. C. T. Souza, A. C. Puhl, L. Martínez, R. Aparicio, A. S. Nascimento, A. C. M. Figueira, P. Nguyen, P. Webb, M. S. Skaf, I. Polikarpov, Identification of a New Hormone Binding Site on the Surface of Thyroid Hormone Receptor. Mol. Endocr. 28(4), 534-545, 2014. [LINK]
    		• M. R. B. Batista, L. Martínez, Dynamics of Nuclear Receptor Helix-12 switch of transcription activation by modeling time-resolved fluorescence anisotropy decays. Biophys. J. 105(7), 1670-1680, 2013. [PDF] [Supplementary Data] [Associated Software]
    		• M. V. Liberato, A. S. Nascimento, S. D. Ayers, J. Z. Lin, R. L. Silveira, L. Martínez, P. C. T. Souza, D. Saidemberg, T. Deng, A. A. Amato, M. Togashi, W. A. Hsueh, K. Phillips, M. S. Palma, F. A. R. Neves, M. S. Skaf, P. Webb, I. Polikarpov, Medium Chain Fatty Acids are Selective Peroxisome Proliferator Activated-γ Activators and Pan-PPAR Partial Agonists. PLoS ONE 7(5): e36297, 2012. [LINK]
    		• L. Martínez, A. C. M. Figueira, I. Polikarpov, M. S. Skaf, Mapping the Intramolecular Vibrational Energy Flow in Proteins Reveals Functionally Important Residues. J. Phys. Chem. Lett. 2, 16, 2073-2078, 2011. [PDF] [Supplementary Information] [Codes]
    		• P. C. T. Souza, G. B. Barra, L. F. R. Velasco, I. C. J. Ribeiro, L. A. Simeoni, M. Togashi, P. Webb, F. A. R. Neves, M. S. Skaf, L. Martínez, I. Polikarpov, Helix 12 dynamics and thyroid hormone receptor's activity: experimental and molecular dynamics studies of Ile280 mutants. J. Mol. Biol. 412, 5, 882-893, 2011. [PDF]
    		• A. C. M. Figueira, D. M. Saidemberg, P. C. T. Souza, L. Martínez, T. S. Scanlan, J. D. Baxter, M. S. Skaf, M. S. Palma, P. Webb, I. Polikarpov, Analysis of agonist and antagonist effects on Thyroid Receptor conformation by Hydrogen/Deuterium-exchange, Mol. Endocrinol. 25, 15-31, 2011. [PDF]
    		• L. Martínez, P. C. T. Souza, W. Silva, R. V. Portugal, A. S. Nascimento, M. Nakahira, L. M. T. R. Lima, I. Polikarpov, M. S. Skaf, On the denaturation mechanisms of the ligand binding domain of thyroid hormone receptors, J. Phys. Chem. B, 114, 1529-1540, 2010. [PDF]
    		• A. S. Araujo, L. Martínez, R. P. Nicolucci, M. S. Skaf, I. Polikarpov, Structural modeling of high-affinity thyroid receptor-ligand complexes, Europ. Biophys. J. 39, 1523-1536, 2010. [PDF]
    		• L. Martínez, A. S. Nascimento, F. M. Nunes, K. Phillips, R. Aparício, S. M. G. Dias, A. C. M. Figueira, J. H. Lin, P. Nguyen, J. W. Apriletti, F. A. R. Neves, J. D. Baxter, P. Webb, M. S. Skaf, I. Polikarpov, Gaining Ligand Selectivity in Thyroid Hormone Receptors via Entropy, Proc. Natl. Acad. Sci USA, 106, 20717-20722, 2009. [PDF] [Supplementary Information] [Associated software]
    		• L. Bleicher, R. Aparício, F. M. Nunes, L. Martínez, S. M. G. Dias, A. C. M. Figueira, M. A. M. Santos, W. H. Venturelli, R. Silva, P. M. Donate, F. A. R. Neves, L. A. Simeoni, J. D. Baxter, P. Webb, M. S. Skaf, I. Polikarpov, Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms, BMC Struct. Biol. 8, 8, 2008. [LINK]
    • M. T. Sonoda, L. Martínez, P. Webb, M. S. Skaf, I. Polikarpov, Ligand Dissociation from Estrogen Receptor Is Mediated by Receptor Dimerization: Evidence from Molecular Dynamics Simulations, Mol. Endocrinol. 22, 1565-1578, 2008. [PDF]
    		• L. Martínez, I. Polikarpov, M. S. Skaf, Only Subtle Protein Conformational Adaptations Are Required for Ligand Binding to Thyroid Hormone Receptors: Simulations Using a Novel Multipoint Steered Molecular Dynamics Approach, J. Phys. Chem. B, 112, 10741-10751, 2008. [PDF] Associated software: [LINK]
    		• L. Martínez, P. Webb, M. S. Skaf, I. Polikarpov, Molecular Dynamics Simulations of Ligand Dissociation from Thyroid Hormone Receptors: Evidence for the Likeliest Escape Pathway and Its Implications for the Design of Novel Ligands, J. Med. Chem. 49, 23-26, 2006. [PDF]
    		• L. Martínez, M. T. Sonoda, P. Webb, J. D. Baxter, M. S. Skaf, I. Polikarpov, Molecular Dynamics Simulations Reveal Multiple Pathways of Ligand Dissociation from Thyroid Hormone Receptors, Biophys. J. 89, 2011-2023, 2005. [PDF]
    		• L. Martínez Simulações de Dinâmica Molecular dos Receptores do Hormônio Tireoidiano. Tese de Doutorado. [PDF]


    Other

    		• R. Farias, U. Arnold, L. Martínez, U. Schuchardt, M. J. D. M. Janini, C. Airoldi, Synthesis, characterization and catalytic properties of sol-gel derived mixed oxides, J. Phys. Chem. Solids 64, 2385-2389, 2003. [PDF]
    		• L. Martínez, Robson F. de Farias, C. Airoldi, Thermochemical data on adducts of copper chloride with the amino acids lysine and glycine, Thermochim. Acta 395, 21-26, 2003. [PDF]
    		• R. Farias, L. Martínez, C. Airoldi, Synthesis, characterization and a thermogravimetric study of copper, cobalt and tin mono- and bis-adducts with ethyleneurea, ethylenethiourea and propyleneurea, Trans. Met. Chem. 27, 748-750, 2002. [PDF]
    		• R. Farias, L. Martínez, C. Airoldi, A calorimetric investigation into copper-arginine and copper-alanine solid state interactions, Trans. Met. Chem. 27, 253-255, 2002. [PDF]
    		• R. Farias, L. Martínez, C. Airoldi, Synthesis, characterization and thermal behavior of 18 cadmium halides adducts involving ethyleneurea, ethylenethiourea and propyleneurea, Thermochim. Acta 376, 91-94, 2001. [PDF]
    		• R. Farias, L. Martínez, C. Airoldi, Decrease of interlamellar spacing of silica samples induced by external pressure, J. Non-Cryst. Solids, 276, 56-60, 2000. [PDF]