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1

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Cheatham, Thomas E., Galindo-Murillo, Rodrigo, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.60 MB

english, 2015

2

Hydrophobic Unnatural Base Pairs Show a Watson-Crick Pairing in Micro-second Molecular Dynamics Simulations

Galindo-Murillo, Rodrigo, Barroso-Flores, Joaquín

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2019

Language:

english

File:

PDF, 1.54 MB

english, 2019

3

Molecular recognition between DNA and a copper-based anticancer complex

Galindo-Murillo, Rodrigo, Ruíz-Azuara, Lena, Moreno-Esparza, Rafael, Cortés-Guzmán, Fernando

Journal:

Physical Chemistry Chemical Physics

Year:

2012

Language:

english

File:

PDF, 2.87 MB

english, 2012

4

π-Stacking between Casiopeinas® and DNA bases

Galindo-Murillo, Rodrigo, Hernandez-Lima, Joseelyne, González-Rendón, Mayra, Cortés-Guzmán, Fernando, Ruíz-Azuara, Lena, Moreno-Esparza, Rafael

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.37 MB

english, 2011

5

DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides

Galindo-Murillo, Rodrigo, Cheatham, Thomas E.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

6

Calix[n]arene-based drug carriers: A DFT study of their electronic interactions with a chemotherapeutic agent used against leukemia

Galindo-Murillo, Rodrigo, Olmedo-Romero, Alberto, Cruz-Flores, Eduardo, Petrar, P.M., Kunsagi-Mate, Sandor, Barroso-Flores, Joaquín

Journal:

Computational and Theoretical Chemistry

Year:

2014

Language:

english

File:

PDF, 1.94 MB

english, 2014

7

Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus

Lin, Zhenjian, Koch, Michael, Abdel Aziz, May Hamdy, Galindo-Murillo, Rodrigo, Tianero, Ma. Diarey, Cheatham, Thomas E., Barrows, Louis R., Reilly, Chris A., Schmidt, Eric W.

Journal:

Organic Letters

Year:

2014

Language:

english

File:

PDF, 850 KB

english, 2014

8

In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study

Galindo-Murillo, Rodrigo, Sandoval-Salinas, María Eugenia, Barroso-Flores, Joaquín

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.81 MB

english, 2014

9

The π-Back-Bonding Modulation and Its Impact in the Electronic Properties of Cu II Antineoplastic Compounds: An Experimental and Theoretical Study

García-Ramos, Juan Carlos, Galindo-Murillo, Rodrigo, Tovar-Tovar, Araceli, Alonso-Saenz, Ana Luisa, Gómez-Vidales, Virginia, Flores-Álamo, Marcos, Ortiz-Frade, Luis, Cortes-Guzmán, Fernando, Moreno-Es

Journal:

Chemistry - A European Journal

Year:

2014

Language:

english

File:

PDF, 963 KB

english, 2014

10

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2015

Language:

english

File:

PDF, 3.78 MB

english, 2015

11

Regrinding and floc-flotation of silver sulphide scavenger concentrate

Espinoza-Ortega, O., Song, S., Lopez-Valdivieso, A., Galindo-Murillo, F., Reyes-Bahena, J. L.

Journal:

Mineral Processing and Extractive Metallurgy

Year:

2003

Language:

english

File:

PDF, 182 KB

english, 2003

12

Potential Amoebicidal Activity of Hydrazone Derivatives: Synthesis, Characterization, Electrochemical Behavior, Theoretical Study and Evaluation of the Biological Activity

Toledano-Magaña, Yanis, García-Ramos, Juan, Navarro-Olivarria, Marisol, Flores-Alamo, Marcos, Manzanera-Estrada, Mayra, Ortiz-Frade, Luis, Galindo-Murillo, Rodrigo, Ruiz-Azuara, Lena, Meléndrez-Luevan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.86 MB

english, 2015

13

129 Convergence and reproducibility of the DNA duplex d(GCACGAACGAACGAACGC) using molecular dynamics simulations

Galindo-Murillo, Rodrigo, Cheatham III, Thomas E.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 260 KB

english, 2015

14

Intercalation processes of copper complexes in DNA

Galindo-Murillo, R., Garcia-Ramos, J. C., Ruiz-Azuara, L., Cheatham, T. E., Cortes-Guzman, F.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.45 MB

english, 2015

15

On the absence of intrahelical DNA dynamics on the μs to ms timescale

Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 1.46 MB

english, 2014

16

Probing the influence of hypermodified residues within the tRNA3Lys anticodon stem loop interacting with the A-loop primer sequence from HIV-1

Galindo-Murillo, Rodrigo, Davis, Darrell R., Cheatham, Thomas E.

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2015

Language:

english

File:

PDF, 1.92 MB

english, 2015

17

Transitions of Double-Stranded DNA Between the A- and B-Forms

Waters, James Thomas, Lu, Xiang-Jun, Galindo-Murillo, Rodrigo, Gumbart, James C., Kim, Harold D., Cheatham, Thomas E., Harvey, Stephen Craig

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 2.62 MB

english, 2016

18

Using Wavelet Analysis to Assist in Identification of Significant Events in Molecular Dynamics Simulations

Heidari, Zahra, Roe, Daniel R, Galindo-Murillo, Rodrigo, Ghasemi, Jahan B., Cheatham, Thomas E.

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 2.09 MB

english, 2016

19

Assessing the current state of AMBER force field modifications for DNA

Galindo-Murillo, Rodrigo, Robertson, James C., Zgarbova, Marie, Sponer, Jiri, Otyepka, Michal, Jurecka, Petr, Cheatham, Thomas E.

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 3.08 MB

english, 2016

20

A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[ N ]arenes as carriers for Bosutinib and Sorafenib

Galindo-Murillo, Rodrigo, Aguilar-Suárez, Luis Enrique, Barroso-Flores, Joaquín

Journal:

Journal of Computational Chemistry

Year:

2016

Language:

english

File:

PDF, 531 KB

english, 2016

21

A Range of Nitrato Coordination Modes in Ni II Complexes with the Versatile Ligand 1,8-Bis(2-pyridyl)-3,6-dithiaoctane: Structural, Spectroscopic, Electrochemical, and Theoretical Studies

Ramírez-Delgado, Vanessa, Hernández-Ayala, Luis Felipe, García-Ramos, Juan Carlos, Flores-Alamo, Marcos, Galindo-Murillo, Rodrigo, Ruiz-Azuara, Lena, Ortiz-Frade, Luis

Journal:

European Journal of Inorganic Chemistry

Year:

2015

Language:

english

File:

PDF, 6.56 MB

english, 2015

22

Polycyclic ferrocenyl(dihydro)thiazepine Derivatives: Diastereo-selective synthesis, Characterization, Electrochemical Behavior, Theoretical and Biological Investigation

Sánchez García, Jessica J., Toledano-Magaña, Yanis, Flores-Alamo, Marcos, Martínez-Klimova, Elena, Galindo-Murillo, Rodrigo, Hernández-Ayala, Luis F., Ortiz-Frade, Luis, García-Ramos, Juan C., Klimova

Journal:

Journal of Inorganic Biochemistry

Year:

2016

Language:

english

File:

PDF, 1.12 MB

english, 2016

23

The isomeric effect on the pharmacokinetic behavior of anticancer Cu(II) mixed chelate complexes: Experimental and Theoretical Approach.

García-Ramos, Juan Carlos, Vértiz-Serrano, Guadalupe, Macías-Rosales, Lucia, Galindo-Murillo, Rodrigo, Toledano-Magaña, Yanis, Bernal, Juan Pablo, Cortés-Guzmán, Fernando, Ruiz-Azuara, Lena

Journal:

European Journal of Inorganic Chemistry

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

24

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

Hayatshahi, Hamed S., Roe, Daniel R., Galindo-Murillo, Rodrigo, Hall, Kathleen B., Cheatham, Thomas E.

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 1.41 MB

english, 2017

25

Water-Soluble Ruthenium (II) Chiral Heteroleptic Complexes with Amoebicidal in Vitro and in Vivo Activity

Toledano-Magaña, Yanis, García-Ramos, Juan C., Torres-Gutiérrez, Carolina, Vázquez-Gasser, Cristina, Esquivel-Sánchez, José M., Flores-Alamo, Marcos, Ortiz-Frade, Luis, Galindo-Murillo, Rodrigo, Nequi

Journal:

Journal of Medicinal Chemistry

Year:

2017

Language:

english

File:

PDF, 2.78 MB

english, 2017

26

Structural and dynamical instability of DNA caused by high occurrence of d5SICS and dNaM unnatural nucleotides

Galindo-Murillo, Rodrigo, Barroso-Flores, Joaquín

Journal:

Physical Chemistry Chemical Physics

Year:

2017

Language:

english

File:

PDF, 3.60 MB

english, 2017

27

The role of DNA-backbone in minor groove ligand binding

Dalia, Díaz-Gómez G., Rodrigo, Galindo-Murillo, Cortes-Guzman, Fernando

Journal:

Year:

2017

Language:

english

File:

PDF, 1.92 MB

english, 2017

28

Synthesis, characterization, theoretical studies and biological activity of coordination compounds with essential metals containing N4-donor ligand 2,9-di(ethylaminomethyl)-1,10-phenanthroline

Hernández-Ayala, Luis Felipe, Flores-Álamo, Marcos, Escalante-Tovar, Sigfrido, Galindo-Murillo, Rodrigo, García-Ramos, Juan Carlos, García-Valdés, Jesús, Gómez-Vidales, Virginia, Reséndiz-Acevedo, Kar

Journal:

Inorganica Chimica Acta

Year:

2017

Language:

english

File:

PDF, 880 KB

english, 2017

29

Effect of tunable redox behavior of bis chelate substituted 1,10-phenantroline Cu(II) complexes on its reaction with superoxide anion in DMSO. Toward a simple criterion to identify a SOD-like mechanism

Manzanera-Estrada, Mayra E., Cruz-Ramírez, Marisela, Flores-Alamo, Marcos, Gracia y Jiménez, José Miguel, Galindo-Murillo, Rodrigo, García-Ramos, Juan Carlos, Ruiz-Azuara, Lena, Ortiz-Frade, Luis

Journal:

Journal of Inorganic Biochemistry

Year:

2017

Language:

english

File:

PDF, 2.01 MB

english, 2017

30

Computational DNA binding studies of (-)-epigallocatechin-3-gallate.

Galindo-Murillo, Rodrigo, Cheatham, Thomas E.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2017

Language:

english

File:

PDF, 3.97 MB

english, 2017

31

Dissociative reactions of benzonorbornadienes with tetrazines: scope of leaving groups and mechanistic insights

Xu, M., Galindo-Murillo, R., Cheatham, T. E., Franzini, R. M.

Journal:

Organic & Biomolecular Chemistry

Year:

2017

Language:

english

File:

PDF, 1.13 MB

english, 2017

32

Defining a conformational ensemble that directs activation of PPARγ

Chrisman, Ian M., Nemetchek, Michelle D., de Vera, Ian Mitchelle S., Shang, Jinsai, Heidari, Zahra, Long, Yanan, Reyes-Caballero, Hermes, Galindo-Murillo, Rodrigo, Cheatham, Thomas E., Blayo, Anne-Lau

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 4.60 MB

english, 2018

33

Exploring potentially alternative non-canonical DNA duplex structures through simulation

Galindo-Murillo, Rodrigo, Cheatham, Thomas E., Hopkins, Robert C.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2018

Language:

english

File:

PDF, 1.85 MB

english, 2018

34

4-HNE carbonylation induces local conformational changes on bovine serum albumin and thioredoxin. A molecular dynamics study

Alviz-Amador, Antistio, Galindo-Murillo, Rodrigo, Pineda-Alemán, Rafael, Pérez-González, Humberto, Rodríguez-Cavallo, Erika, Vivas-Reyes, Ricardo, Méndez-Cuadro, Darío

Journal:

Journal of Molecular Graphics and Modelling

Year:

2018

Language:

english

File:

PDF, 4.19 MB

english, 2018

35

Development and benchmark to obtain AMBER parameters dataset for non-standard amino acids modified with 4-hydroxy-2-nonenal

Alviz-Amador, Antistio, Galindo-Murillo, Rodrigo, Pineda-Alemán, Rafael, Pérez-González, Humberto, Rodríguez-Cavallo, Erika, Vivas-Reyes, Ricardo, Méndez-Cuadro, Darío

Journal:

Year:

2018

Language:

english

File:

PDF, 832 KB

english, 2018

36

Antigiardiasic activity of Cu(II) coordination compounds: Redox imbalance and membrane damage after a short exposure time

Rufino-González, Yadira, Ponce-Macotela, Martha, García-Ramos, Juan Carlos, Martínez-Gordillo, Mario N., Galindo-Murillo, Rodrigo, González-Maciel, Angelica, Reynoso-Robles, Rafael, Tovar-Tovar, Arace

Journal:

Journal of Inorganic Biochemistry

Year:

2019

Language:

english

File:

PDF, 1.58 MB

english, 2019

37

Pharmacophoric sites of anticancer metal complexes located using quantum topological atomic descriptors

Ramírez-Palma, Lillian G., García-Jacas, César R., García-Ramos, Juan C., Almada-Monter, Ricardo, Galindo-Murillo, Rodrigo, Cortés-Guzmán, Fernando

Journal:

Journal of Molecular Structure

Year:

2019

Language:

english

File:

PDF, 1.83 MB

english, 2019

38

Pharmacophoric sites of anticancer metal complexes located using quantum topological atomic descriptors

Ramírez-Palma, Lillian G., García-Jacas, César R., García-Ramos, Juan C., Almada-Monter, Ricardo, Galindo-Murillo, Rodrigo, Cortés-Guzmán, Fernando

Journal:

Journal of Molecular Structure

Year:

2019

File:

PDF, 1.83 MB

2019

39

Heteroleptic NiII complexes: Synthesis, structural characterization, computational studies and amoebicidal activity evaluation

HernÃ¡ndez-Ayala, Luis Felipe, Toledano-MagaÃ±a, Yanis, Ortiz-Frade, Luis, Flores-Alamo, Marcos, Galindo-Murillo, Rodrigo, Reina, Miguel, GarcÃa-Ramos, Juan Carlos, Ruiz-Azuara, Lena

Journal:

Journal of Inorganic Biochemistry

Year:

2020

Language:

english

File:

PDF, 1.86 MB

english, 2020

40

AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal

Alviz-Amador, Antistio, Galindo-Murillo, Rodrigo, PÃ©rez-GonzÃ¡lez, Humberto, RodrÃguez-Cavallo, Erika, Vivas-Reyes, Ricardo, MÃ©ndez-Cuadro, DarÃo

Journal:

Year:

2020

File:

PDF, 862 KB

2020

41

Novel Blocker of Onco SK3 Channels Derived from Scorpion Toxin Tamapin and Active against Migration of Cancer Cells

Mayorga-Flores, Marlen, ChantÃ´me, AurÃ©lie, Melchor-Meneses, Carolina Monserrath, Domingo, Isabelle, Titaux-Delgado, Gustavo Alfredo, Galindo-Murillo, Rodrigo, Vandier, Christophe, del RÃo-Portilla,

Journal:

ACS Medicinal Chemistry Letters

Year:

2020

File:

PDF, 1.60 MB

2020

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