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Molecular Dynamics Simulation
110
"Cyclase-associated protein 1 (CAP1) is a prenyl-binding partner of Rap1 GTPase" (2018) Zhang, X.;Cao, S.;Barila, G. (...)Altschuler, D.L. Journal of Biological Chemistry. 293(20)
"Calcium interactions with Cx26 hemmichannel: Spatial association between MD simulations biding sites and variant pathogenicity" (2018) Albano, J.M.R.;Mussini, N.;Toriano, R. (...)Pickholz, M. Computational Biology and Chemistry. 77:331-342
"V-Shaped Molecular Configuration of Wax Esters of Jojoba Oil in a Langmuir Film Model" (2018) Caruso, B.; Martini, M.F.; Pickholz, M.; Perillo, M.A. Langmuir. 34(26):7887-7898
"Frustration, function and folding" (2018) Ferreiro, D.U.; Komives, E.A.; Wolynes, P.G. Current Opinion in Structural Biology. 48:68-73
"Studies of 4-arylthiazolylhydrazones derived from 1-indanones as Trypanosoma cruzi squalene epoxidase inhibitors by molecular simulations" (2018) Noguera, G.J.; Fabian, L.E.; Lombardo, E.; Finkielsztein, L.M. Organic and Biomolecular Chemistry. 16(44):8525-8536
"Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps" (2018) Marsico, F.;Burastero, O.;Defelipe, L.A. (...)Marti, M.A. Biochemical and Biophysical Research Communications. 498(2):305-312
"A sumatriptan coarse-grained model to explore different environments: interplay with experimental techniques" (2018) Wood, I.;Albano, J.M.R.;Filho, P.L.O. (...)Pickholz, M. European Biophysics Journal. 47(5):561-571
"Solvents to fragments to drugs: MD applications in drug design" (2018) Defelipe, L.A.;Arcon, J.P.;Modenutti, C.P. (...)Barril, X. Molecules. 23(12)
"Understanding the molecular basis of the high oxygen affinity variant human hemoglobin Coimbra" (2018) Jorge, S.E.;Bringas, M.;Petruk, A.A. (...)Estrin, D. Archives of Biochemistry and Biophysics. 637:73-78
"Structural and mechanistic comparison of the Cyclopropane Mycolic Acid Synthases (CMAS) protein family of Mycobacterium tuberculosis" (2018) Defelipe, L.A.; Osman, F.; Marti, M.A.; Turjanski, A.G. Biochemical and Biophysical Research Communications. 498(2):288-295
"Synthesis and activity evaluation of a series of cholanamides as modulators of the liver X receptors" (2018) Martínez, M.D.;Ghini, A.A.;Dansey, M.V. (...)Burton, G. Bioorganic and Medicinal Chemistry. 26(5):1092-1101
"Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation" (2017) Bartesaghi, S.;Herrera, D.;Martinez, D.M. (...)Radi, R. Archives of Biochemistry and Biophysics. 622:9-25
"Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions" (2017) Arcon, J.P.;Defelipe, L.A.;Modenutti, C.P. (...)Martí, M.A. Journal of Chemical Information and Modeling. 57(4):846-863
"Fluorinated oxysterol analogues: Synthesis, molecular modelling and LXRβ activity" (2017) Rodriguez, C.R.;Alvarez, L.D.;Dansey, M.V. (...)Burton, G. Journal of Steroid Biochemistry and Molecular Biology. 165:268-276
"Access and Binding of H2S to Hemeproteins: The Case of HbI of Lucina pectinata" (2016) Boubeta, F.M.; Bari, S.E.; Estrin, D.A.; Boechi, L. Journal of Physical Chemistry B. 120(36):9642-9653
"Impact of human galectin-1 binding to saccharide ligands on dimer dissociation kinetics and structure" (2016) Romero, J.M.;Trujillo, M.;Estrin, D.A. (...)Di Lella, S. Glycobiology. 26(12):1317-1327
"PrxQ B from Mycobacterium tuberculosis is a monomeric, thioredoxin-dependent and highly efficient fatty acid hydroperoxide reductase" (2016) Reyes, A.M.;Vazquez, D.S.;Zeida, A. (...)Trujillo, M. Free Radical Biology and Medicine. 101:249-260
"CG2AA: Backmapping protein coarse-grained structures" (2016) Lombardi, L.E.; Martí, M.A.; Capece, L. Bioinformatics. 32(8):1235-1237
"The Dynamic Behavior of the P2X4 Ion Channel in the Closed Conformation" (2016) Pierdominici-Sottile, G.; Moffatt, L.; Palma, J. Biophysical Journal. 111(12):2642-2650
"Binding of the substrate UDP-glucuronic acid induces conformational changes in the xanthan gum glucuronosyltransferase" (2016) Salinas, S.R.;Petruk, A.A.;Brukman, N.G. (...)Ielpi, L. Protein Engineering, Design and Selection. 29(6):197-207
"Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics" (2016) Parra, R.G.;Schafer, N.P.;Radusky, L.G. (...)Ferreiro, D.U. Nucleic acids research. 44(W1):W356-W360
"The N-terminal pre-A region of Mycobacterium tuberculosis 2/2HbN promotes NO-dioxygenase activity" (2016) Pesce, A.;Bustamante, J.P.;Bidon-Chanal, A. (...)Nardini, M. FEBS Journal. 283(2):305-322
"Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain" (2016) Rinaldi, J.;Arrar, M.;Sycz, G. (...)Goldbaum, F.A. Journal of Molecular Biology. 428(6):1165-1179
"Steered Molecular Dynamics Methods Applied to Enzyme Mechanism and Energetics" (2016) Ramírez, C.L.; Martí, M.A.; Roitberg, A.E. Methods in Enzymology. 578:123-143
"Theoretical investigation of the mechanism of nitroxyl decomposition in aqueous solution" (2016) Bringas, M.; Semelak, J.; Zeida, A.; Estrin, D.A. Journal of Inorganic Biochemistry. 162:102-108
"Anti-hemagglutinin antibody derived lead peptides for inhibitors of influenza virus binding" (2016) Memczak, H.;Lauster, D.;Kar, P. (...)Stöcklein, W.F.M. PLoS ONE. 11(7)
"Dynamics of dissipative self-assembly of particles interacting through oscillatory forces" (2016) Tagliazucchi, M.; Szleifer, I. Faraday Discussions. 186:399-418
"Exploring the molecular basis of action of ring D aromatic steroidal antiestrogens" (2015) Alvarez, L.D.; Veleiro, A.S.; Burton, G. Proteins: Structure, Function and Bioinformatics. 83(7):1297-1306
"WATCLUST: A tool for improving the design of drugs based on protein-water interactions" (2015) López, E.D.;Arcon, J.P.;Gauto, D.F. (...)Turjanski, A.G. Bioinformatics. 31(22):3697-3699
"The E. Coli thioredoxin folding mechanism: The key role of the C-terminal helix" (2015) Vazquez, D.S.;Sánchez, I.E.;Garrote, A. (...)Santos, J. Biochimica et Biophysica Acta - Proteins and Proteomics. 1854(2):127-137
"Molecular mechanism of myoglobin autoxidation: Insights from computer simulations" (2015) Arcon, J.P.;Rosi, P.;Petruk, A.A. (...)Estrin, D.A. Journal of Physical Chemistry A. 119(5):1802-1813
"Molecular Dynamics Study of Ionic Liquids Complexation within β-Cyclodextrins" (2015) Semino, R.; Rodríguez, J. Journal of Physical Chemistry B. 119(14):4865-4872
"Equilibrium and Dynamical Characteristics of Imidazole Langmuir Monolayers on Graphite Sheets" (2015) Rodriguez, J.; Elola, M.D.; Laria, D. Journal of Physical Chemistry B. 119(29):9123-9128
"Molecular Basis of Hydroperoxide Specificity in Peroxiredoxins: The Case of AhpE from Mycobacterium tuberculosis" (2015) Zeida, A.;Reyes, A.M.;Lichtig, P. (...)Trujillo, M. Biochemistry. 54(49):7237-7247
"Exploring the molecular basis of neurosteroid binding to the β3 homopentameric GABAA receptor" (2015) Alvarez, L.D.; Estrin, D.A. Journal of Steroid Biochemistry and Molecular Biology. 154:159-167
"Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO" (2015) Howes, B.D.;Boechi, L.;Boffi, A. (...)Smulevich, G. Advances in microbial physiology. 67:85-126
"Reactivity of inorganic sulfide species toward a heme protein model" (2015) Bieza, S.A.;Boubeta, F.;Feis, A. (...)Bari, S.E. Inorganic Chemistry. 54(2):527-533
"Engineered chimeras reveal the structural basis of hexacoordination in globins: A case study of neuroglobin and myoglobin" (2015) Boron, I.;Capece, L.;Pennacchietti, F. (...)Nadra, A.D. Biochimica et Biophysica Acta - General Subjects. 1850(1):169-177
"Bridging Theory and Experiment to Address Structural Properties of Truncated Haemoglobins: Insights from Thermobifida fusca HbO" (2015) Howes, B.D.;Boechi, L.;Boffi, A. (...)Smulevich, G. Advances in Microbial Physiology
"Efficient calculation of enzyme reaction free energy profiles using a hybrid differential relaxation algorithm: Application to mycobacterial zinc hydrolases" (2015) Romero, J.M.;Martin, M.;Ramirez, C.L. (...)Karabencheva-Christova T. Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions, 2015. 100:33-65
"Effects of dimethyl sulfoxide on lipid membrane electroporation" (2014) Fernández, M.L.; Reigada, R. Journal of Physical Chemistry B. 118(31):9306-9312
"Interaction between proteins and Ir based CO releasing molecules: Mechanism of adduct formation and CO release" (2014) Petruk, A.A.;Vergara, A.;Marasco, D. (...)Merlino, A. Inorganic Chemistry. 53(19):10456-10462
"Tracking the molecular evolution of calcium permeability in a nicotinic acetylcholine receptor" (2014) Lipovsek, M.;Fierro, A.;Pérez, E.G. (...)Elgoyhen, A.B. Molecular Biology and Evolution. 31(12):3250-3265
"Molecular basis of thermal stability in truncated (2/2) hemoglobins" (2014) Bustamante, J.P.;Bonamore, A.;Nadra, A.D. (...)Boechi, L. Biochimica et Biophysica Acta - General Subjects. 1840(7):2281-2288
"QM/MM study of the C-C coupling reaction mechanism of CYP121, an essential Cytochrome p450 of Mycobacterium tuberculosis" (2014) Dumas, V.G.;Defelipe, L.A.;Petruk, A.A. (...)Marti, M.A. Proteins: Structure, Function and Bioinformatics. 82(6):1004-1021
"Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework" (2014) Morzan, U.N.;Ramírez, F.F.;Oviedo, M.B. (...)Lebrero, M.C.G. Journal of Chemical Physics. 140(16)
"Interplay of the H-bond donor-acceptor role of the distal residues in hydroxyl ligand stabilization of Thermobifida fusca truncated hemoglobin" (2014) Nicoletti, F.P.;Bustamante, J.P.;Droghetti, E. (...)Smulevich, G. Biochemistry. 53(51):8021-8030
"Mechanistic insight into the enzymatic reduction of truncated hemoglobin N of Mycobacterium tuberculosis: Role of the CD loop and Pre-A motif in electron cycling" (2014) Singh, S.;Thakur, N.;Oliveira, A. (...)Dikshit, K.L. Journal of Biological Chemistry. 289(31):21573-21583
"Underlying Thermodynamics of pH-Dependent Allostery" (2014) Di Russo, N.V.; Martí, M.A.; Roitberg, A.E. Journal of Physical Chemistry B. 118(45):12818-12826
"Structural basis of redox-dependent modulation of galectin-1 dynamics and function" (2014) Guardia, C.M.;Caramelo, J.J.;Trujillo, M. (...)Rabinovich, G.A. Glycobiology. 24(5):428-441
"The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer" (2014) Alvarez-Paggi, D.; Zitare, U.; Murgida, D.H. Biochimica et Biophysica Acta - Bioenergetics. 1837(7):1196-1207
"H-bonding networks of the distal residues and water molecules in the active site of Thermobifida fusca hemoglobin" (2013) Nicoletti, F.P.;Droghetti, E.;Howes, B.D. (...)Smulevich, G. Biochimica et Biophysica Acta - Proteins and Proteomics. 1834(9):1901-1909
"Effect of the protonation degree of a self-assembled monolayer on the immobilization dynamics of a [NiFe] hydrogenase" (2013) Utesch, T.;Millo, D.;Castro, M.A. (...)Mroginski, M.A. Langmuir. 29(2):673-682
"Quaternary structure effects on the hexacoordination equilibrium in rice hemoglobin rHb1: Insights from molecular dynamics simulations" (2013) Morzan, U.N.; Capece, L.; Marti, M.A.; Estrin, D.A. Proteins: Structure, Function and Bioinformatics. 81(5):863-873
"Host-guest molecular interactions in vanillin/amylose inclusion complexes" (2013) Rodríguez, S.D.; Bernik, D.L. Applied Spectroscopy. 67(8):884-891
"Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study" (2013) Jara, G.E.; Vera, D.M.A.; Pierini, A.B. Journal of Molecular Graphics and Modelling. 46:10-21
"27-Nor-Δ4-dafachronic acid is a synthetic ligand of Caenorhabditis elegans DAF-12 receptor" (2013) Samaja, G.A.;Castro, O.;Alvarez, L.D. (...)Burton, G. Bioorganic and Medicinal Chemistry Letters. 23(10):2893-2896
"Molecular basis of the NO trans influence in quaternary T-state human hemoglobin: A computational study" (2013) Petruk, A.A.; Vergara, A.; Estrin, D.; Merlino, A. FEBS Letters. 587(15):2393-2398
"Excess protons in water-acetone mixtures. II. A conductivity study" (2013) Semino, R.; Longinotti, M.P. Journal of Chemical Physics. 139(16)
"Solvent structure improves docking prediction in lectin-carbohydrate complexes" (2013) Gauto, D.F.;Petruk, A.A.;Modenutti, C.P. (...)Martí, M.A. Glycobiology. 23(2):241-258
"Mechanism of cysteine oxidation by peroxynitrite: An integrated experimental and theoretical study" (2013) Zeida, A.;González Lebrero, M.C.;Radi, R. (...)Estrin, D.A. Archives of Biochemistry and Biophysics. 539(1):81-86
"Electrostatically driven second-sphere ligand switch between high and low reorganization energy forms of native cytochrome c" (2013) Alvarez-Paggi, D.;Castro, M.A.;Tórtora, V. (...)Murgida, D.H. Journal of the American Chemical Society. 135(11):4389-4397
"Loop A Is Critical for the Functional Interaction of Two Beta vulgaris PIP Aquaporins" (2013) Jozefkowicz, C.;Rosi, P.;Sigaut, L. (...)Alleva, K. PLoS ONE. 8(3)
"Size-controlled nanopores in lipid membranes with stabilizing electric fields" (2012) Fernández, M.L.; Risk, M.; Reigada, R.; Vernier, P.T. Biochemical and Biophysical Research Communications. 423(2):325-330
"The Caenorhabditis elegans DAF-12 nuclear receptor: Structure, dynamics, and interaction with ligands" (2012) Alvarez, L.D.; Mañez, P.A.; Estrin, D.A.; Burton, G. Proteins: Structure, Function and Bioinformatics. 80(7):1798-1809
"Protein Stability and Dynamics Modulation: The Case of Human Frataxin" (2012) Roman, E.A.;Faraj, S.E.;Gallo, M. (...)Santos, J. PLoS ONE. 7(9)
"New insight into the electrochemical desorption of alkanethiol SAMs on gold" (2012) Pensa, E.;Vericat, C.;Grumelli, D. (...)Méndez De Leo, L.P. Physical Chemistry Chemical Physics. 14(35):12355-12367
"Molecular basis of the mechanism of thiol oxidation by hydrogen peroxide in aqueous solution: Challenging the S N2 paradigm" (2012) Zeida, A.;Babbush, R.;González Lebrero, M.C. (...)Estrin, D.A. Chemical Research in Toxicology. 25(3):741-746
"Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations" (2011) Boron, I.;Russo, R.;Boechi, L. (...)Nadra, A.D. IUBMB Life. 63(3):206-213
"Structure of supercooled water in clusters and bulk and its relation to the two-state picture of water: results from the TIP4P-ice model." (2011) Constantin, J.G.;Fris, A.R.;Appignanesi, G. (...)Corti, H. The European physical journal. E, Soft matter. 34(11):126
"Protein dynamics and ligand migration interplay as studied by computer simulation" (2011) Arroyo-Mañez, P.;Bikiel, D.E.;Boechi, L. (...)Petruk, A.A. Biochimica et Biophysica Acta - Proteins and Proteomics. 1814(8):1054-1064
"The peculiar heme pocket of the 2/2 hemoglobin of cold-adapted Pseudoalteromonas haloplanktis TAC125" (2011) Howes, B.D.;Giordano, D.;Boechi, L. (...)Smulevich, G. Journal of Biological Inorganic Chemistry. 16(2):299-311
"Structural basis for ligand recognition in a mushroom lectin: Solvent structure as specificity predictor" (2011) Gauto, D.F.;Di Lella, S.;Estrin, D.A. (...)Martí, M.A. Carbohydrate Research. 346(7):939-948
"Biological activity and ligand binding mode to the progesterone receptor of A-homo analogues of progesterone" (2011) Alvarez, L.D.;Dansey, M.V.;Martí, M.A. (...)Burton, G. Bioorganic and Medicinal Chemistry. 19(5):1683-1691
"Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins" (2011) Forti, F.; Boechi, L.; Estrin, D.A.; Marti, M.A. Journal of Computational Chemistry. 32(10):2219-2231
"Exploring the molecular basis of human manganese superoxide dismutase inactivation mediated by tyrosine 34 nitration" (2011) Moreno, D.M.;Martí, M.A.;De Biase, P.M. (...)Boechi, L. Archives of Biochemistry and Biophysics. 507(2):304-309
"Molecular basis for the substrate stereoselectivity in tryptophan dioxygenase" (2011) Capece, L.;Lewis-Ballester, A.;Marti, M.A. (...)Yeh, S.-R. Biochemistry. 50(50):10910-10918
"Structure of supercooled water in clusters and bulk and its relation to the two-state picture of water: Results from the TIP4P-ice model" (2011) Gelman Constantin, J.;Rodriguez Fris, A.;Appignanesi, G. (...)Corti, H. European Physical Journal E. 34(11)
"An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network" (2011) Guardia, C.M.A.;Gauto, D.F.;Di Lella, S. (...)Estrin, D.A. Journal of Chemical Information and Modeling. 51(8):1918-1930
"Electron transfer dynamics of Rhodothermus marinus caa 3 cytochrome c domains on biomimetic films" (2011) Molinas, M.F.;De Candia, A.;Szajnman, S.H. (...)Murgida, D.H. Physical Chemistry Chemical Physics. 13(40):18088-18098
"Anomalies in supercooled NaCl aqueous solutions: A microscopic perspective" (2011) Longinotti, M.P.; Carignano, M.A.; Szleifer, I.; Corti, H.R. Journal of Chemical Physics. 134(24)
"Fluoride as a probe for h-bonding interactions in the active site of heme proteins: The case of thermobifida fusca hemoglobin" (2011) Nicoletti, F.P.;Droghetti, E.;Boechi, L. (...)Smulevich, G. Journal of the American Chemical Society. 133(51):20970-20980
"Aqueous electrolytes confined within functionalized silica nanopores" (2011) Videla, P.E.;Sala, J.;Mart, J. (...)Laria, D. Journal of Chemical Physics. 135(10)
"P38γ activation triggers dynamical changes in allosteric docking sites" (2011) Rodriguez Limardo, R.G.;Ferreiro, D.N.;Roitberg, A.E. (...)Turjanski, A.G. Biochemistry. 50(8):1384-1395
"Sulfide binding properties of truncated hemoglobins" (2010) Nicoletti, F.P.;Comandini, A.;Bonamore, A. (...)Boffi, A. Biochemistry. 49(10):2269-2278
"Copper-transfer mechanism from the human chaperone Atox1 to a metal-binding domain of wilson disease protein" (2010) Rodriguez-Granillo, A.; Crespo, A.; Estrin, D.A.; Wittung-Stafshede, P. Journal of Physical Chemistry B. 114(10):3698-3706
"Insights on glucocorticoid receptor activity modulation through the binding of rigid steroids" (2010) Presman, D.M.;Alvarez, L.D.;Levi, V. (...)Pecci, A. PLoS ONE. 5(10)
"The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer" (2010) Stojković, V.;Perissinotti, L.L.;Lee, J. (...)Kohen, A. Chemical Communications. 46(47):8974-8976
"Substrate stereo-specificity in tryptophan dioxygenase and indoleamine 2,3-dioxygenase" (2010) Capece, L.;Arrar, M.;Roitberg, A.E. (...)Estrin, D.A. Proteins: Structure, Function and Bioinformatics. 78(14):2961-2972
"Structure of Yeast Regulatory Subunit: A Glimpse into the Evolution of PKA Signaling" (2010) Rinaldi, J.;Wu, J.;Yang, J. (...)Taylor, S.S. Structure. 18(11):1471-1482
"Structural transitions and dipole moment of water clusters (H 2 O) n=4-100" (2010) Gelman-Constantin, J.;Carignano, M.A.;Szleifer, I. (...)Corti, H.R. Journal of Chemical Physics. 133(2)
"Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case" (2010) Boechi, L.;Mañez, P.A.;Javier Luque, F. (...)Estrin, D.A. Proteins: Structure, Function and Bioinformatics. 78(4):962-970
"The first step of the dioxygenation reaction carried out by tryptophan dioxygenase and indoleamine 2,3-dioxygenase as revealed by quantum mechanical/molecular mechanical studies" (2010) Capece, L.;Lewis-Ballester, A.;Batabyal, D. (...)Marti, M.A. Journal of Biological Inorganic Chemistry. 15(6):811-823
"Molecular basis of coupled protein and electron transfer dynamics of cytochrome c in biomimetic complexes" (2010) Alvarez-Paggi, D.;Martín, D.F.;Debiase, P.M. (...)Murgida, D.H. Journal of the American Chemical Society. 132(16):5769-5778
"Thermal fluctuations determine the electron-transfer rates of cytochrome c in electrostatic and covalent complexes" (2010) Ly, H.K.;Marti, M.A.;Martin, D.F. (...)Murgida, D.H. ChemPhysChem. 11(6):1225-1235
"Molecular basis for the electric field modulation of cytochrome c structure and function" (2009) De Biase, P.M.;Paggi, D.A.;Doctorovich, F. (...)Marti, M.A. Journal of the American Chemical Society. 131(44):16248-16256
"Exploring the picosecond time domain of the solvation dynamics of coumarin 153 within β-cyclodextrins" (2008) Rodriguez, J.; Martí, J.; Guardia, E.; Laria, D. Journal of Physical Chemistry B. 112(30):8990-8998
"A molecular dynamics simulation study of hydrogen bonding in aqueous ionic solutions" (2005) Guàrdia, E.; Martí, J.; García-Tarrés, L.; Laria, D. Journal of Molecular Liquids. 117(1-3):63-67