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Correlations between dynamics, structure and function in protein: computer simulations and algorithms

Grant number: 10/16947-9
Support Opportunities:Regular Research Grants
Duration: December 01, 2010 - November 30, 2012
Field of knowledge:Biological Sciences - Biophysics - Molecular Biophysics
Principal Investigator:Leandro Martinez
Grantee:Leandro Martinez
Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Articles published in Agência FAPESP Newsletter about the research grant:
Articles published in other media outlets (0 total):
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VEICULO: TITULO (DATA)
VEICULO: TITULO (DATA)

Scientific publications (39)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
DE OLIVEIRA, IVAN PIRES; MARTINEZ, LEANDRO. The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation. Physical Chemistry Chemical Physics, v. 22, n. 1, p. 354-367, . (17/02201-4, 18/24293-0, 10/16947-9, 13/08293-7)
DOS SANTOS, RICARDO N.; BOTTINO, GUILHERME F.; GOZZO, FABIO C.; MORCOS, FARUCK; MARTINEZ, LEANDRO. Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 88, n. 4, . (18/14274-9, 10/16947-9, 15/13667-9, 18/24293-0, 13/08293-7, 14/17264-3)
DE OLIVEIRA, IVAN PIRES; LESCANO, CAROLINE HONAISER; DE NUCCI, GILBERTO. In Silico Mapping of Essential Residues in the Catalytic Domain of PDE5 Responsible for Stabilization of Its Commercial Inhibitors. SCIENTIA PHARMACEUTICA, v. 87, n. 4, . (13/22360-9, 10/16947-9, 13/08293-7, 13/05475-7, 17/02201-4, 17/26687-3)
BOTTINO, GUILHERME F.; FERRARI, ALLAN J. R.; GOZZO, FABIO C.; MARTINEZ, LEANDRO. Structural discrimination analysis for constraint selection in protein modeling. Bioinformatics, v. 37, n. 21, p. 3766-3773, . (13/08293-7, 16/13195-2, 19/17007-4, 10/16947-9, 18/14274-9)
PEREIRA, ANDER F.; PICCOLI, VINICIUS; MARTINEZ, LEANDRO. Trifluoroethanol direct interactions with protein backbones destabilize a-helices. JOURNAL OF MOLECULAR LIQUIDS, v. 365, p. 11-pg., . (20/04549-0, 20/04916-3, 18/14274-9, 18/24293-0, 13/08293-7, 10/16947-9)
PICCOLI, VINICIUS; MARTINEZ, LEANDRO. Correlated counterion effects on the solvation of proteins by ionic liquids. JOURNAL OF MOLECULAR LIQUIDS, v. 320, p. 16-pg., . (18/24293-0, 13/08293-7, 10/16947-9)
PICCOLI, VINICIUS; MARTINEZ, LEANDRO. Ionic liquid solvation of proteins in native and denatured states. JOURNAL OF MOLECULAR LIQUIDS, v. 363, p. 15-pg., . (20/04916-3, 13/08293-7, 18/24293-0, 18/14274-9, 10/16947-9)
SIQUEIRA, TAYANE HONORATO; MARTINEZ, LEANDRO. Molecular simulations of fluconazole-mediated inhibition of sterol biosynthesis. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, . (10/16947-9, 13/08293-7)
MARTINEZ, LEANDRO. MEASURING THE CONDUCTIVITY OF VERY DILUTE ELECTROLYTE SOLUTIONS, DROP BY DROP. Química Nova, v. 41, n. 7, p. 4-pg., . (13/08293-7, 13/05475-7, 10/16947-9)
SEGATO, FERNANDO; BERTO, GABRIELA L.; DE ARAUJO, EVANDRO ARES; MUNIZ, JOAO RENATO; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-beta-1,4-glucanase from glycoside hydrolase family 12. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 70, p. 4-pg., . (09/52840-7, 08/05637-9, 10/16947-9)
SIQUEIRA, TAYANE HONORATO; MARTINEZ, LEANDRO. Molecular simulations of fluconazole-mediated inhibition of sterol biosynthesis. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, v. 38, n. 6, p. 11-pg., . (13/08293-7, 10/16947-9)
MARTINEZ, LEANDRO. MEASURING THE CONDUCTIVITY OF VERY DILUTE ELECTROLYTE SOLUTIONS, DROP BY DROP. Química Nova, v. 41, n. 7, p. 814-817, . (13/05475-7, 10/16947-9, 13/08293-7)
JARA, GABRIEL E.; MARTINEZ, LEANDRO. Anthrax Edema Factor: An Ion-Adaptive Mechanism of Catalysis with Increased Transition-State Conformational Flexibility. Journal of Physical Chemistry B, v. 120, n. 27, p. 6504-6514, . (13/08293-7, 13/05475-7, 13/22360-9, 10/16947-9)
DOS SANTOS, RICARDO N.; FERRARI, ALLAN J. R.; DE JESUS, HUGO C. R.; GOZZO, FABIO C.; MORCOS, FARUCK; MARTINEZ, LEANDRO. Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics, v. 34, n. 13, p. 2201-2208, . (13/08293-7, 13/05475-7, 16/13195-2, 14/17264-3, 15/13667-9, 10/16947-9)
CAMPOS, LIVIA WEIJENBORG; ZENATTI, PRISCILA PINI; PISSINATO, LEONARDO GRANATO; RODRIGUES, GISELE O. LIBANIO; ARTICO, LEONARDO LUIS; GUIMARAES, THAIS RAFAEL; ARCHANGELO, LETICIA FROHLICH; MARTINEZ, LEANDRO; BROOKS, ANDREW J.; YUNES, JOSE ANDRES. Oncogenic basic amino acid insertions at the extracellular juxtamembrane region of IL7RA cause receptor hypersensitivity. Blood, v. 133, n. 11, p. 1259-1263, . (12/12802-1, 14/20015-5, 10/16947-9, 13/08293-7)
LOPEZ, ALVARO J.; MARTINEZ, LEANDRO. Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations. Journal of Computational Chemistry, v. 39, n. 19, p. 1249-1258, . (13/08293-7, 13/05475-7, 10/16947-9)
MARTINEZ, LEANDRO. Introducing the Levinthal's Protein Folding Paradox and Its Solution. Journal of Chemical Education, v. 91, n. 11, p. 1918-1923, . (13/05475-7, 10/16947-9)
FERRARI, ALLAN J. R.; GOZZO, FABIO C.; MARTINEZ, LEANDRO. Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints. Bioinformatics, v. 35, n. 17, p. 3005-3012, . (13/08293-7, 13/05475-7, 18/14274-9, 16/13195-2, 14/17264-3, 13/23814-3, 10/16947-9)
FERRARI, ALLAN J. R.; CLASEN, MILAN A.; KURT, LOUISE; CARVALHO, PAULO C.; GOZZO, FABIO C.; MARTINEZ, LEANDRO. TopoLink: evaluation of structural models using chemical crosslinking distance constraints. Bioinformatics, v. 35, n. 17, p. 3169-3170, . (13/08293-7, 13/05475-7, 18/14274-9, 16/13195-2, 10/16947-9)
DE OLIVEIRA, IVAN PIRES; LESCANO, CAROLINE HONAISER; DE NUCCI, GILBERTO. Q817G mutation in phosphodiesterase type 5: Conformational analysis and dissociation profile of the inhibitor Tadalafil. CHEMICAL BIOLOGY & DRUG DESIGN, v. 93, n. 4, p. 419-429, . (13/08293-7, 13/05475-7, 10/16947-9)
BIRGIN, ERNESTO G.; MARTINEZ, J. M.; MARTINEZ, LEANDRO; ROCHA, GERD B.. Sparse Projected-Gradient Method As a Linear-Scaling Low-Memory Alternative to Diagonalization in Self-Consistent Field Electronic Structure Calculations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 9, n. 2, p. 1043-1051, . (06/53768-0, 08/00468-4, 10/16947-9)
SEGATO, FERNANDO; BERTO, GABRIELA L.; DE ARAUJO, EVANDRO ARES; MUNIZ, JOAO RENATO; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-beta-1,4-glucanase from glycoside hydrolase family 12. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 70, n. 2, p. 267-270, . (08/05637-9, 09/52840-7, 10/16947-9)
LOPEZ, ALVARO J.; BARROS, EMILIA P.; MARTINEZ, LEANDRO. On the Interpretation of subtilisin Carlsberg Time-Resolved Fluorescence Anisotropy Decays: Modeling with Classical Simulations. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 747-755, . (13/08293-7, 18/24293-0, 10/16947-9)
PICCOLI, VINICIUS; MARTINEZ, LEANDRO. Correlated counterion effects on the solvation of proteins by ionic liquids. JOURNAL OF MOLECULAR LIQUIDS, v. 320, n. A, . (18/24293-0, 10/16947-9, 13/08293-7)
DE OLIVEIRA, IVAN PIRES; JARA, GABRIEL ERNESTO; MARTINEZ, LEANDRO. Molecular mechanism of activation of Burkholderia cepacia lipase at aqueous-organic interfaces. Physical Chemistry Chemical Physics, v. 19, n. 46, p. 31499-31507, . (13/08293-7, 13/05475-7, 13/22360-9, 10/16947-9)
MARTINEZ, LEANDRO; SHIMIZU, SEISHI. Molecular Interpretation of Preferential Interactions in Protein Solvation: A Solvent-Shell Perspective by Means of Minimum-Distance Distribution Functions. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 13, n. 12, p. 6358-6372, . (13/08293-7, 13/05475-7, 10/16947-9)
CENSONI, LUCIANO; MARTINEZ, LEANDRO. Prediction of kinetics of protein folding with non-redundant contact information. Bioinformatics, v. 34, n. 23, p. 4034-4038, . (13/08293-7, 13/05475-7, 10/16947-9)
CENSONI, LUCIANO; MUNIZ, HELOISA DOS SANTOS; MARTINEZ, LEANDRO. A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics, v. 33, n. 14, p. 2106-2113, . (13/05475-7, 10/16947-9, 13/08293-7)
LESCANO, CAROLINE HONAISER; DE OLIVEIRA, IVAN PIRES; ZAMINELLI, TIAGO; BALDIVIA, DEBORA DA SILVA; DA SILVA, LUAN RAMOS; NAPOLITANO, MAURO; MENDES SILVERIO, CAMILA BITENCOURT; LINCOPAN, NILTON; SANJINEZ-ARGANDONA, ELIANA JANET. Campomanesia adamantium Peel Extract in Antidiarrheal Activity: The Ability of Inhibition of Heat-Stable Enterotoxin by Polyphenols. PLoS One, v. 11, n. 10, . (13/08293-7, 13/05475-7, 10/16947-9)
SONORA, MARTIN; MARTINEZ, LEANDRO; PANTANO, SERGIO; MACHADO, MATIAS R.. Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 61, n. 1, p. 408-422, . (10/16947-9, 13/08293-7, 18/14274-9, 18/24293-0)
OLIVEIRA, IVAN P.; MARTINEZ, LEANDRO. Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea. Physical Chemistry Chemical Physics, v. 18, n. 31, p. 21797-21808, . (10/16947-9, 13/08293-7, 13/05475-7)
MINO-GALAZ, GERMAN A.. Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study. Journal of Physical Chemistry B, v. 119, n. 20, p. 6179-6189, . (13/05475-7, 10/16947-9)
BATISTA, MARIANA R. B.; MARTINEZ, LEANDRO. Dynamics of Nuclear Receptor Helix-12 Switch of Transcription Activation by Modeling Time-Resolved Fluorescence Anisotropy Decays. BIOPHYSICAL JOURNAL, v. 105, n. 7, p. 1670-1680, . (10/16947-9)
LIMA, LEONARDO H. F.; SERPA, VIVIANE I.; ROSSETO, FLAVIO R.; SARTORI, GERALDO RODRIGUES; DE OLIVEIRA NETO, MARIO; MARTINEZ, LEANDRO; POLIKARPOV, IGOR. Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum. Cellulose, v. 20, n. 4, p. 1573-1585, . (09/52840-7, 07/08706-9, 08/56255-9, 08/05637-9, 10/16947-9)
BLEICHER, LUCAS; PRATES, ERICA T.; GOMES, THIAGO C. F.; SILVEIRA, RODRIGO L.; NASCIMENTO, ALESSANDRO S.; ROJAS, ADRIANA L.; GOLUBEV, ALEXANDER; MARTINEZ, LEANDRO; SKAF, MUNIR S.; POLIKARPOV, IGOR. Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations. Journal of Physical Chemistry B, v. 115, n. 24, p. 7940-7949, . (10/08680-2, 09/14107-6, 10/18849-4, 10/16947-9)
SILVEIRA, RODRIGO L.; MARTINEZ, JULIAN; SKAF, MUNIR S.; MARTINEZ, LEANDRO. Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide. Journal of Physical Chemistry B, v. 116, n. 19, p. 5671-5678, . (10/08680-2, 10/16947-9)

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