Search Results - "Andrés, G"

Classical Electrostatics for Biomolecular Simulations by Cisneros, G. Andrés, Karttunen, Mikko, Ren, Pengyu, Sagui, Celeste

“…Electrostatic methods for classical biomolecular simulations are detailed. Among the methods used are Ewald summations, fast multipole and charge-group methods…”
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Mechanistic Elucidation of Zirconium-Catalyzed Direct Amidation by Lundberg, Helena, Tinnis, Fredrik, Zhang, Jiji, Algarra, Andrés G, Himo, Fahmi, Adolfsson, Hans

“…The mechanism of the zirconium-catalyzed condensation of carboxylic acids and amines for direct formation of amides was studied using kinetics, NMR…”
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Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity by Chatterjee, Shubham, Nochebuena, Jorge, Cisneros, G. Andrés

“…Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in…”
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Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study by Maghsoud, Yazdan, Dong, Chao, Cisneros, G. Andrés

“…Xanthine oxidoreductase (XOR) is an enzyme found in various organisms. It converts hypoxanthine to xanthine and urate, which are crucial steps in purine…”
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Sex‐specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination by Bain, Stevie A., Marshall, Hollie, Filia, Andrés G., Laetsch, Dominik R., Husnik, Filip, Ross, Laura

“…Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate…”
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Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat by Maghsoud, Yazdan, Dong, Chao, Cisneros, G. Andrés

“…Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It interconverts xanthine to uric acid as the last step of purine catabolism…”
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Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations by Torabifard, Hedieh, Cisneros, G Andrés

“…Ten-eleven translocation 2 (TET2) is an Fe/α-ketoglutarate (α-KG) dependent enzyme that dealkylates 5-methylcytosine (5mC). The reaction mechanism involves a…”
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Synthesis, Electronic Structure, and Magnetism of [Ni(6-Mes)2]+: A Two-Coordinate Nickel(I) Complex Stabilized by Bulky N‑Heterocyclic Carbenes by Poulten, Rebecca C, Page, Michael J, Algarra, Andrés G, Le Roy, Jennifer J, López, Isidoro, Carter, Emma, Llobet, Antoni, Macgregor, Stuart A, Mahon, Mary F, Murphy, Damien M, Murugesu, Muralee, Whittlesey, Michael K

“…The two-coordinate cationic Ni(I) bis-N-heterocyclic carbene complex [Ni(6-Mes)2]Br (1) [6-Mes…”
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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields by Lagardère, Louis, Jolly, Luc-Henri, Lipparini, Filippo, Aviat, Félix, Stamm, Benjamin, Jing, Zhifeng F, Harger, Matthew, Torabifard, Hedieh, Cisneros, G Andrés, Schnieders, Michael J, Gresh, Nohad, Maday, Yvon, Ren, Pengyu Y, Ponder, Jay W, Piquemal, Jean-Philip

“…We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable…”
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Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects by Maghsoud, Yazdan, Jayasinghe-Arachchige, Vindi M., Kumari, Pratibha, Cisneros, G. Andrés, Liu, Jin

“…The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two…”
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Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids by Vázquez-Montelongo, Erik Antonio, Vázquez-Cervantes, José Enrique, Cisneros, G Andrés

“…Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems…”
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LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields by Kratz, Eric G., Walker, Alice R., Lagardère, Louis, Lipparini, Filippo, Piquemal, Jean-Philip, Andrés Cisneros, G.

“…We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM…”
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Development of Imidazolium-Based Parameters for AMOEBA-IL by Vázquez-Cervantes, José Enrique, Cisneros, G. Andrés

“…A new approach for the efficient parametrization of the polarizable ionic liquid potential AMOEBA-IL and its application to develop parameters for…”
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Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ by Maghsoud, Yazdan, Roy, Arkanil, Leddin, Emmett M., Cisneros, G. Andrés

“…Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy,…”
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Bacterial cellulose films production by Kombucha symbiotic community cultured on different herbal infusions by Ramírez Tapias, Yuly A., Di Monte, M. Victoria, Peltzer, Mercedes A., Salvay, Andrés G.

“…•By-product of Kombucha beverage as a resource of active materials.•Symbiotic Community Of Bacteria and Yeast SCOBY produced bacterial cellulose films.•Sugared…”
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Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields by Nochebuena, Jorge, Piquemal, Jean-Philip, Liu, Shubin, Cisneros, G. Andrés

“…Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields…”
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Programmable microbial ink for 3D printing of living materials produced from genetically engineered protein nanofibers by Duraj-Thatte, Anna M., Manjula-Basavanna, Avinash, Rutledge, Jarod, Xia, Jing, Hassan, Shabir, Sourlis, Arjirios, Rubio, Andrés G., Lesha, Ami, Zenkl, Michael, Kan, Anton, Weitz, David A., Zhang, Yu Shrike, Joshi, Neel S.

“…Living cells have the capability to synthesize molecular components and precisely assemble them from the nanoscale to build macroscopic living functional…”
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Distal Mutations in the β‑Clamp of DNA Polymerase III Disrupt DNA Orientation and Affect Exonuclease Activity by Berger, Madison B., Cisneros, G. Andrés

“…DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase…”
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Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials by Nochebuena, Jorge, Naseem‐Khan, Sehr, Cisneros, G. Andrés

“…Quantum mechanics/molecular mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM…”
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Dissecting the Essential Role of Anomeric β‑Triflates in Glycosylation Reactions by Santana, Andrés G, Montalvillo-Jiménez, Laura, Díaz-Casado, Laura, Corzana, Francisco, Merino, Pedro, Cañada, Francisco J, Jiménez-Osés, Gonzalo, Jiménez-Barbero, Jesús, Gómez, Ana M, Asensio, Juan Luis

“…Glycosylations promoted by triflate-generating reagents are widespread synthetic methods for the construction of glycosidic scaffolds and glycoconjugates of…”
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