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1

GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations

Bachega, José Fernando R., Timmers, Luís Fernando S. M., Assirati, Lucas, Bachega, Leonardo R., Field, Martin J., Wymore, Troy

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 898 KB

english, 2013

2

Genomic risk prediction of aromatase inhibitor-related arthralgia in patients with breast cancer using a novel machine-learning algorithm

Reinbolt, Raquel E., Sonis, Stephen, Timmers, Cynthia D., Fernández-Martínez, Juan Luis, Cernea, Ana, de Andrés-Galiana, Enrique J., Hashemi, Sepehr, Miller, Karin, Pilarski, Robert, Lustberg, Maryam

Journal:

Cancer Medicine

Year:

2017

Language:

english

File:

PDF, 383 KB

english, 2017

3

Genomic Databases and the Search of Protein Targets for Protozoan Parasites

Timmers, Luis Fernando, Pauli, Ivani, Barcellos, Guy, Rocha, Kelen, Caceres, Rafael, de Azevedo Jr., Walter, Soares, Milena

Journal:

Current Drug Targets

Year:

2009

Language:

english

File:

PDF, 131 KB

english, 2009

4

Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs

Nunes, JosÃ© E. S., Duque, Mario A., de Freitas, Talita F., Galina, Luiza, Timmers, Luis F. S. M., Bizarro, Cristiano V., Machado, Pablo, Basso, Luiz A., Ducati, Rodrigo G.

Journal:

Year:

2020

Language:

english

File:

PDF, 4.76 MB

english, 2020

5

Molecular modeling and dynamics simulations of PNP from Streptococcus agalactiae

Rafael Andrade Caceres, Luis Fernando Saraiva Timmers, Raquel Dias, Luiz Augusto Basso, Diogenes Santiago Santos, Walter Filgueira de Azevedo Jr.

Journal:

Bioorganic & Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 689 KB

english, 2008

6

Molecular modeling, dynamics and docking studies of Purine Nucleoside Phosphorylase from Streptococcus pyogenes

Luis Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres, Raquel Dias, Luiz Augusto Basso, Diogenes Santiago Santos, Walter Filgueira de Azevedo Jr

Journal:

Biophysical Chemistry

Year:

2009

Language:

english

File:

PDF, 959 KB

english, 2009

7

Molecular modeling and dynamics studies of cytidylate kinase fromMycobacterium tuberculosisH37Rv

Rafael Andrade Caceres, Luís Fernando Saraiva Macedo Timmers, Ana Luiza Vivan, Cristopher Zandoná Schneider, Luiz Augusto Basso, Walter Filgueira De Azevedo, Diogenes Santiago Santos

Journal:

Journal of Molecular Modeling

Year:

2008

Language:

english

File:

PDF, 315 KB

english, 2008

8

Molecular modeling and dynamics studies of purine nucleoside phosphorylase fromBacteroides fragilis

Ivani Pauli, Luis Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira de Azevedo Jr.

Journal:

Journal of Molecular Modeling

Year:

2009

Language:

english

File:

PDF, 556 KB

english, 2009

9

Combining molecular dynamics and docking simulations of the cytidine deaminase fromMycobacterium tuberculosisH37Rv

Luís Fernando Saraiva Macedo Timmers, Rodrigo Gay Ducati, Zilpa Adriana Sánchez-Quitian, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira de Azevedo

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 554 KB

english, 2012

10

Cooperation and profit allocation in distribution chains

Luis A. Guardiola, Ana Meca, Judith Timmer

Journal:

Decision Support Systems

Year:

2007

Language:

english

File:

PDF, 328 KB

english, 2007

11

Structural studies of human purine nucleoside phosphorylase: Towards a new specific empirical scoring function

Luis Fernando Saraiva Macedo Timmers, Rafael Andrade Caceres, Ana Luiza Vivan, Lisandra Marques Gava, Raquel Dias, Rodrigo Gay Ducati, Luiz Augusto Basso, Diogenes Santiago Santos, Walter Filgueira de

Journal:

Archives of Biochemistry and Biophysics

Year:

2008

Language:

english

File:

PDF, 741 KB

english, 2008

12

Crystal structure determination and dynamic studies of Mycobacterium tuberculosis Cytidine deaminase in complex with products

Zilpa A. Sánchez-Quitian, Luís F.S.M. Timmers, Rafael A. Caceres, Jacqueline G. Rehm, Claudia E. Thompson, Luiz A. Basso, Walter F. de Azevedo Jr., Diógenes S. Santos

Journal:

Archives of Biochemistry and Biophysics

Year:

2011

Language:

english

File:

PDF, 1.37 MB

english, 2011

13

Crystal structure and molecular dynamics studies of purine nucleoside phosphorylase from Mycobacterium tuberculosis associated with acyclovir

Rafael A. Caceres, Luís F.S.M. Timmers, Rodrigo G. Ducati, Diego O.N. da Silva, Luiz A. Basso, Walter F. de Azevedo Jr., Diógenes S. Santos

Journal:

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

14

Crystal structure and molecular dynamics studies of human purine nucleoside phosphorylase complexed with 7-deazaguanine

Rafael Andrade Caceres, Luis Fernando Saraiva Macedo Timmers, Ivani Pauli, Lisandra Marques Gava, Rodrigo Gay Ducati, Luiz Augusto Basso, Diógenes Santiago Santos, Walter Filgueira de Azevedo Jr.

Journal:

Journal of Structural Biology

Year:

2010

Language:

english

File:

PDF, 950 KB

english, 2010

15

Discovery of New Inhibitors of Mycobacterium tuberculosis InhA Enzyme Using Virtual Screening and a 3D-Pharmacophore-Based Approach

Pauli, Ivani, dos Santos, Ricardo N., Rostirolla, Diana C., Martinelli, Leonardo K., Ducati, Rodrigo G., Timmers, Luís F. S. M., Basso, Luiz A., Santos, Diógenes S., Guido, Rafael V. C., Andricopulo,

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 770 KB

english, 2013

16

Design of Novel Potent Inhibitors of Human Uridine Phosphorylase-1: Synthesis, Inhibition Studies, Thermodynamics, and in Vitro Influence on 5-Fluorouracil Cytotoxicity

Renck, Daiana, Machado, Pablo, Souto, Andre A., Rosado, Leonardo A., Erig, Thais, Campos, Maria M., Farias, Caroline B., Roesler, Rafael, Timmers, Luis F. S. M., de Souza, Osmar N., Santos, Diogenes S

Journal:

Journal of Medicinal Chemistry

Year:

2013

Language:

english

File:

PDF, 1.93 MB

english, 2013

17

Kinetic mechanism and energetics of binding of phosphoryl group acceptors to Mycobacterium tuberculosis cytidine monophosphate kinase

Jaskulski, Léia, Rosado, Leonardo A., Rostirolla, Diana C., Timmers, Luis F.S.M., de Souza, Osmar N., Santos, Diogenes S., Basso, Luiz A.

Journal:

Archives of Biochemistry and Biophysics

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

18

Biochemical and Cellular Analysis of Human Variants of the DYT1 Dystonia Protein, TorsinA/TOR1A

Hettich, Jasmin, Ryan, Scott D., de Souza, Osmar Norberto, Saraiva Macedo Timmers, Luís Fernando, Tsai, Shelun, Atai, Nadia A., da Hora, Cintia C., Zhang, Xuan, Kothary, Rashmi, Snapp, Erik, Ericsson,

Journal:

Year:

2014

Language:

english

File:

PDF, 726 KB

english, 2014

19

Piperazine derivatives: Synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase and SAR studies

Rotta, Mariane, Pissinate, Kenia, Villela, Anne Drumond, Back, Davi Fernando, Timmers, Luis Fernando Saraiva Macedo, Bachega, José Fernando Ruggiero, de Souza, Osmar Norberto, Santos, Diógenes Santiag

Journal:

European Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 8.52 MB

english, 2015

20

Regioselectively controlled synthesis of 3(5)-(trifluoromethyl)pyrazolylbenzenesulfonamides and their effects on a pathological pain model in mice

Lobo, Marcio M., Oliveira, Sara M., Brusco, Indiara, Machado, Pablo, Timmers, Luis F.S.M., de Souza, Osmar N., Martins, Marcos A.P., Bonacorso, Hélio G., dos Santos, Josiane M., Canova, Bruna, da Silv

Journal:

European Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 893 KB

english, 2015

21

Bioinformatics Tools for Screening of Antiparasitic Drugs

de Azevedo Junior, Walter Filgueira, Dias, Raquel, Macedo Timmers, Luis Fernando, Pauli, Ivani, Caceres, Rafael, Pereira Soares, Milena

Journal:

Current Drug Targets

Year:

2009

Language:

english

File:

PDF, 178 KB

english, 2009

22

Molecular Modeling as a Tool for Drug Discovery

Barcellos, Guy, Pauli, Ivani, Caceres, Rafael, Macedo Timmers, Luis Fernando, Dias, Raquel, de Azevedo Jr, Walter

Journal:

Current Drug Targets

Year:

2008

Language:

english

File:

PDF, 268 KB

english, 2008

23

In Silico and In Vitro: Identifying New Drugs

Pauli, Ivani, Macedo Timmers, Luis, Caceres, Rafael, Pereira Soares, Milena, de Azevedo Jr., Walter

Journal:

Current Drug Targets

Year:

2008

Language:

english

File:

PDF, 223 KB

english, 2008

24

Mycobacterium tuberculosis histidinol dehydrogenase: biochemical characterization and inhibition studies

Lunardi, Juleane, Martinelli, Leonardo Kras Borges, Raupp, Alessandra Silva, Nunes, José Eduardo Sacconi, Rostirolla, Diana Carolina, Timmers, Luis Fernando Saraiva Macedo, Villela, Anne Drumond, Piss

Journal:

Year:

2016

Language:

english

File:

PDF, 1.96 MB

english, 2016

25

Molecular Recognition Models: A Challenge to Overcome

Caceres, Rafael, Pauli, Ivani, Macedo Timmers, Luis Fernando, de Azevedo Jr., Walter

Journal:

Current Drug Targets

Year:

2008

Language:

english

File:

PDF, 168 KB

english, 2008

26

Protein-Drug Interaction Studies for Development of Drugs Against Plasmodium falciparum

de Azevedo Jr., Walter, Caceres, Rafael, Pauli, Ivani, Timmers, Luis Fernando, Barcellos, Guy, Rocha, Kelen, Soares, Milena

Journal:

Current Drug Targets

Year:

2009

Language:

english

File:

PDF, 226 KB

english, 2009

27

Drug-Binding Databases

Macedo Timmers, Luis Fernando, Pauli, Ivani, Caceres, Rafael, de Azevedo Jr., Walter

Journal:

Current Drug Targets

Year:

2008

Language:

english

File:

PDF, 126 KB

english, 2008

28

EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies

Timmers, Luís Fernando Saraiva Macedo, Neto, Antônio M. S., Montalvão, Rinaldo W., Basso, Luiz A., Santos, Diógenes S., Norberto de Souza, Osmar

Journal:

Journal of Molecular Modeling

Year:

2017

Language:

english

File:

PDF, 2.44 MB

english, 2017

29

Observed crowding effects on Mycobacterium tuberculosis 2-trans-enoyl-ACP (CoA) reductase enzyme activity are not due to excluded volume only

Rotta, Mariane, Timmers, Luis F. S. M., Sequeiros-Borja, Carlos, Bizarro, Cristiano V., de Souza, Osmar N., Santos, Diogenes S., Basso, Luiz A.

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 2.16 MB

english, 2017

30

Activity of 2-(quinolin-4-yloxy)acetamides in mycobacterium tuberculosis clinical isolates and identification of their molecular target by whole genome sequencing

Subtil, Fernanda Teixeira, Villela, Anne Drumond, Abbadi, Bruno Lopes, Rodrigues-Junior, Valnês S., Bizarro, Cristiano Valim, Timmers, Luis Fernando Saraiva Macedo, de Souza, Osmar Norberto, Pissinate

Journal:

International Journal of Antimicrobial Agents

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

31

Thermodynamics, functional and structural characterization of inosine–uridine nucleoside hydrolase from Leishmania braziliensis

Dalberto, Pedro Ferrari, Martinelli, Leonardo Kras Borges, Bachega, Jose Fernando Ruggiero, Timmers, Luis Fernando Saraiva Macedo, Pinto, Antonio Frederico Michel, Dadda, Adilio da Silva, Petersen, Gu

Journal:

Year:

2017

Language:

english

File:

PDF, 893 KB

english, 2017

32

Searching for potential mTOR inhibitors: ligand-based drug design, docking and molecular dynamics studies of rapamycin binding site

Kist, Roger, Timmers, Luis Fernando Saraiva Macedo, Caceres, Rafael Andrade

Journal:

Journal of Molecular Graphics and Modelling

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

33

A Network Flow Approach to Predict Protein Targets and Flavonoid Backbones to Treat Respiratory Syncytial Virus Infection

Vargas, José Eduardo, Puga, Renato, Poloni, Joice de Faria, Saraiva Macedo Timmers, Luis Fernando, Porto, Barbara Nery, Norberto de Souza, Osmar, Bonatto, Diego, Condessa Pitrez, Paulo Márcio, Tetelbo

Journal:

BioMed Research International

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

34

Pre-clinical evaluation of quinoxaline-derived chalcones in tuberculosis

Muradás, Thaís C., Abbadi, Bruno L., Villela, Anne D., Macchi, Fernanda S., Bergo, Pedro F., de Freitas, Talita F., Sperotto, Nathalia D. M., Timmers, Luis F. S. M., Norberto de Souza, Osmar, Picada,

Journal:

Year:

2018

Language:

english

File:

PDF, 2.21 MB

english, 2018

35

Reducing external costs of nitrogen pollution by relocation of pig production between regions in the European Union

van Grinsven, Hans J. M., van Dam, Jan D., Lesschen, Jan Peter, Timmers, Marloes H. G., Velthof, Gerard L., Lassaletta, Luis

Journal:

Regional Environmental Change

Year:

2018

Language:

english

File:

PDF, 1.78 MB

english, 2018

36

Correction to: Reducing external costs of nitrogen pollution by relocation of pig production between regions in the European Union

van Grinsven, Hans J. M., van Dam, Jan D., Lesschen, Jan Peter, Timmers, Marloes H. G., Velthof, Gerard L., Lassaletta, Luis

Journal:

Regional Environmental Change

Year:

2019

Language:

english

File:

PDF, 116 KB

english, 2019

37

The importance of the quaternary structure to represent conformational ensembles of the major Mycobacterium tuberculosis drug target

Tarabini, Renata Fioravanti, Timmers, Luís Fernando Saraiva Macedo, Sequeiros-Borja, Carlos Eduardo, Norberto de Souza, Osmar

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 3.28 MB

english, 2019

38

Structural modelling of the equine protein disulphide isomerase A1 and its quantification in the epididymis and seminal plasma

Linden, Liana de Salles, Bustamante-Filho, Ivan Cunha, Souza, Ana Paula Binato, Lopes, TaynÃ¡ NauÃª, Silva, Anna FlÃ¡via Tischer, TomÃ©, Luise Marcon, Timmers, Luis Fernando Macedo Saraiva, Santos, SÃ

Journal:

Year:

2020

File:

PDF, 1.31 MB

2020

39

Microbial Î²âGalactosidases of industrial importance: Computational studies on the effects of point mutations on the lactose hydrolysis reaction

Coelho de Andrade, Bruna, Saraiva Macedo Timmers, Luis Fernando, Renard, Gaby, Volpato, Giandra, Volken de Souza, Claucia Fernanda

Journal:

Biotechnology Progress

Year:

2020

Language:

english

File:

PDF, 2.45 MB

english, 2020

40

How far can we go with herbicides that rely on classic modes of action?

Sperotto, Raul Antonio, Timmers, Luis Fernando Saraiva Macedo

Journal:

Year:

2020

File:

PDF, 376 KB

2020

41

Theoretical characterization of the shikimate 5-dehydrogenase reaction from Mycobacterium tuberculosis by hybrid QC/MM simulations and quantum chemical descriptors

Grillo, Igor Barden, Bachega, JosÃ© Fernando Ruggiero, Timmers, Luis Fernando S. M., Caceres, Rafael A., de Souza, Osmar Norberto, Field, Martin J., Rocha, Gerd Bruno

Journal:

Journal of Molecular Modeling

Year:

2020

File:

PDF, 2.08 MB

2020

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