Structural and dynamic properties of guanosine-analog binding to 2′-deoxyguanosine-II riboswitch: a computational study D Antunes, LHS Santos, ER Caffarena, ACR Guimarães Journal of Biomolecular Structure and Dynamics 43 (17), 9654-9675 , 2025 2025 Citations: 3
Long‐Term Impact of the Largest Environmental Disaster in Latin America (Fundão Dam Failure) on Microbial Communities in Lakes of the Doce River Basin, Brazil P Almeida, A Torres, M Gomes, E Caffarena, H Jesus, P Pereira, ... Environmental Microbiology 27 (9), e70171 , 2025 2025
The Extended N-Terminal Domain of VPAC1 Isoform 2 Acts as a Self-inhibitory Element: Insights from Molecular Dynamics Simulations MH Reis, D Antunes, IBS Martins, ER Caffarena Brazilian Congress on Bioinformatics, 74-89 , 2025 2025
Free Energy Perturbation and Free-Energy Calculations Applied to Drug Design D Antunes, LH Santos, ACR Guimarães, ER Caffarena Computer-Aided and Machine Learning-Driven Drug Design: From Theory to … , 2025 2025 Citations: 3
Genome-Wide Exploration of Thiamin Pyrophosphate Riboswitches in Medically Relevant Fungi Reveals Diverse Distribution and Implications for Antimicrobial Drug Targeting V Vargas-Junior, ACR Guimarães, ER Caffarena, D Antunes ACS omega 9 (51), 50134-50146 , 2024 2024
Riboswitches as Antimicrobial Targets V Vargas-Junior, E Caffarena, D Antunes Structure-Based Drug Design, 81-108 , 2024 2024 Citations: 2
Structural Characterization of Heat Shock Protein 90β and Molecular Interactions with Geldanamycin and Ritonavir: A Computational Study CR Lima, D Antunes, E Caffarena, N Carels International Journal of Molecular Sciences 25 (16), 8782 , 2024 2024 Citations: 4
Exploring Novel Antimalarial Compounds Targeting Plasmodium falciparum Enoyl-ACP Reductase: Computational and Experimental Insights G AR Oliveira, B GDV Morales, R MO Sousa, S S Pereira, D Antunes, ... ACS omega 9 (21), 22777-22793 , 2024 2024 Citations: 6
PACAP key interactions with PAC1, VPAC1, and VPAC2 identified by molecular dynamics simulations FATP Meireles, D Antunes, JR Temerozo, DC Bou-Habib, ER Caffarena Journal of Biomolecular Structure and Dynamics 42 (6), 3128-3144 , 2024 2024 Citations: 4
Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β‐glucosidase probed by multiple MD and computational approaches REO Rocha, DCB Mariano, TS Almeida, LS CorrêaCosta, PHC Fischer, ... Proteins: Structure, Function, and Bioinformatics 91 (2), 218-236 , 2023 2023 Citations: 8
In silico investigation of riboswitches in fungi: structural and dynamical insights into TPP riboswitches in Aspergillus oryzae V Vargas-Junior, D Antunes, AC Guimarães, E Caffarena RNA biology 19 (1), 90-103 , 2022 2022 Citations: 10
pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations LH Santos, ER Caffarena, RS Ferreira Journal of Biomolecular Structure and Dynamics 40 (20), 10359-10372 , 2022 2022 Citations: 5
Combining network-based and matrix factorization to predict novel drug-target interactions: a case study using the brazilian natural chemical database RS Martins, MF da Costa Gomes, ER Caffarena Current Bioinformatics 17 (9), 793-803 , 2022 2022 Citations: 2
RASopathy cohort of patients enrolled in a Brazilian reference center for rare diseases: a novel familial LZTR1 variant and recurrent mutations NC Rabelo, ME Gomes, I de Oliveira Moraes, JC Pfisterer, GL de Morais, ... The Application of Clinical Genetics 15, 153 , 2022 2022 Citations: 10
Differences in Charge Distribution in Leishmania tarentolae Leishmanolysin Result in a Reduced Enzymatic Activity V Ennes-Vidal, D Antunes, E Poláková, V Yurchenko, SSC Oliveira, ... International Journal of Molecular Sciences 23 (14), 7660 , 2022 2022 Citations: 4
Development of New Potential Inhibitors of β1 Integrins through In Silico Methods—Screening and Computational Validation D Vasconcelos, B Chaves, A Albuquerque, L Andrade, A Henriques, ... Life 12 (7), 932 , 2022 2022 Citations: 6
Bacterial 2′-deoxyguanosine riboswitch classes as potential targets for antibiotics: a structure and dynamics study D Antunes, LHS Santos, ER Caffarena, ACR Guimarães International Journal of Molecular Sciences 23 (4), 1925 , 2022 2022 Citations: 10
RASopathy cohort of patients enrolled in a Brazilian reference center for rare diseases: a novel familial LZTR1 variant and recurrent mutations RN Chaves, ME Gomes, I de Oliveira Moraes, PJ Cantagalli, ... The Application of Clinical Genetics 15, 153 , 2022 2022 Citations: 2
RASopathy cohort of patients enrolled in a Brazilian reference center for rare diseases: a novel familial LZTR1 variant and recurrent mutations N Chaves Rabelo, ME Gomes, I de Oliveira Moraes, J Cantagalli Pfisterer, ... The Application of Clinical Genetics, 153-170 , 2022 2022 Citations: 6
How does alpha 1 Histidine102 affect the binding of modulators to alpha 1 beta 2 gamma 2 GABA A receptors? molecular insights from in silico experiments M Julia Amundarain, ER Caffarena, M Daniel Costabel PHYSICAL CHEMISTRY CHEMICAL PHYSICS 23 (6), 3993-4006 , 2021 2021
MOST CITED SCHOLAR PUBLICATIONS
Boosting docking-based virtual screening with deep learning JC Pereira, ER Caffarena, CN Dos Santos Journal of chemical information and modeling 56 (12), 2495-2506 , 2016 2016 Citations: 452
Integrating molecular docking and molecular dynamics simulations LHS Santos, RS Ferreira, ER Caffarena Docking screens for drug discovery, 13-34 , 2019 2019 Citations: 343
Elastic properties, Young's modulus determination and structural stability of the tropocollagen molecule: a computational study by steered molecular dynamics AC Lorenzo, ER Caffarena Journal of biomechanics 38 (7), 1527-1533 , 2005 2005 Citations: 204
Evaluation of 7-arylaminopyrazolo [1, 5-a] pyrimidines as anti-Plasmodium falciparum, antimalarial, and Pf-dihydroorotate dehydrogenase inhibitors LFSP Azeredo, JP Coutinho, VAP Jabor, PR Feliciano, MC Nonato, ... European Journal of Medicinal Chemistry 126, 72-83 , 2017 2017 Citations: 92
Toll-like receptor 1 N248S single-nucleotide polymorphism is associated with leprosy risk and regulates immune activation during mycobacterial infection C de Sales Marques, VN Brito-de-Souza, LTA Guerreiro, JH Martins, ... The Journal of infectious diseases 208 (1), 120-129 , 2013 2013 Citations: 72
Hydrogen Bonding of carboxylic acids in aqueous solutions—UV spectroscopy, viscosity, and molecular simulation of acetic acid G Ruderman, ER Caffarena, IG Mogilner, EJ Tolosa Journal of solution chemistry 27 (10), 935-948 , 1998 1998 Citations: 68
Genomic and structural features of the yellow fever virus from the 2016–2017 Brazilian outbreak MM Gómez, FVS Abreu, AAC Santos, IS Mello, MP Santos, IP Ribeiro, ... Journal of General Virology 99 (4), 536-548 , 2018 2018 Citations: 66
Caracterização do envelhecimento populacional no município do Rio de Janeiro: contribuições para políticas públicas sustentáveis DSB Alves, MTS Barbosa, ER Caffarena, AS Silva Cadernos Saúde Coletiva 24, 63-69 , 2016 2016 Citations: 57
Epoxy-α-Lapachone Has In Vitro and In Vivo Anti-Leishmania (Leishmania) amazonensis Effects and Inhibits Serine Proteinase Activity in This Parasite F Souza-Silva, SC Bourguignon, BAS Pereira, LMC Côrtes, ... Antimicrobial agents and chemotherapy 59 (4), 1910-1918 , 2015 2015 Citations: 48
In silico analysis of the V66M variant of human BDNF in psychiatric disorders: An approach to precision medicine CCS De Oliveira, GRC Pereira, JYS De Alcantara, D Antunes, ... Plos one 14 (4), e0215508 , 2019 2019 Citations: 47
Glass transition in aqueous solutions of glucose. Molecular dynamics simulation ER Caffarena, JR Grigera Carbohydrate research 300 (1), 51-57 , 1997 1997 Citations: 47
Using RNA sequence and structure for the prediction of riboswitch aptamer: a comprehensive review of available software and tools D Antunes, NAN Jorge, ER Caffarena, F Passetti Frontiers in genetics 8, 231 , 2018 2018 Citations: 44
Naturally occurring genetic variants of human caspase‐1 differ considerably in structure and the ability to activate interleukin‐1β H Luksch, MJ Romanowski, O Chara, V Tüngler, ER Caffarena, ... Human mutation 34 (1), 122-131 , 2013 2013 Citations: 44
Structural and molecular modeling features of P2X receptors LA Alves, JHM Da Silva, DNM Ferreira, AA Fidalgo-Neto, PCN Teixeira, ... International journal of molecular sciences 15 (3), 4531-4549 , 2014 2014 Citations: 43
Hydration of glucose in the rubbery and glassy states studied by molecular dynamics simulation ER Caffarena, JR Grigera Carbohydrate research 315 (1-2), 63-69 , 1999 1999 Citations: 42
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors LH Santos, RS Ferreira, ER Caffarena Memórias do Instituto Oswaldo Cruz 110 (7), 847-864 , 2015 2015 Citations: 41
On the hydrogen bond structure of water at different densities ER Caffarena, JR Grigera Physica A: Statistical Mechanics and its Applications 342 (1-2), 34-39 , 2004 2004 Citations: 40
Understanding structure–activity relationships for trypanosomal cysteine protease inhibitors by simulations and free energy calculations LH Santos, BJ Waldner, JE Fuchs, GAN Pereira, KR Liedl, ER Caffarena, ... Journal of Chemical Information and Modeling 59 (1), 137-148 , 2018 2018 Citations: 37
Synthesis, antimalarial evaluation and molecular modeling studies of hydroxyethylpiperazines, potential aspartyl protease inhibitors, part 2 W Cunico, CRB Gomes, V Facchinetti, M Moreth, C Penido, ... European journal of medicinal chemistry 44 (9), 3816-3820 , 2009 2009 Citations: 37
Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants AM Maia, JHM da Silva, AL Mencalha, ER Caffarena, E Abdelhay BMC bioinformatics 13 (1), 184 , 2012 2012 Citations: 33
