About MSSM
(Modelagem e Simulação de Sistemas Moleculares)

Our research at MSSM (Modeling and Simulation of Molecular Systems) focuses on the development and application of molecular models and computational methods. We pay special attention to molecular dynamics (MD) simulation and force field development. MD simulation consists in numerically solving Newton’s equation of motion. In classical MD, an empirical potential energy function, namely a force field, is employed to describe the interactions between a system of particles. The quality of which basically determines the accuracy of such simulations provided that an adequate sampling is achieved. More specifically, our group currently aims at four research lines: (i) the development of force fields for simulating biological and nanotechnological systems; (ii) the development of novel nature-inspired optimization techniques based on evolutionary approaches; (iii) the applications towards biological systems such as virus proteins and chemokines; and (iv) the simulation of nanosystems for drug delivery applications.

Research Topics

Development of force fields for simulating biological and nanotechnological systems
Development of novel nature-inspired optimization techniques based on evolutionary approaches
Applications towards biological systems such as Zika virus proteins and chemokines
Simulation of nanosystems for drug delivery applications

Publications

 

2019

Póvoa, RCBL; Koshiyama, AS; Dias, DM; Souza, PL; Horta, BAC
Unimodal optimization using a genetic-programming-based method with periodic boundary conditions. Genet. Program Evol. M. (submitted)

Gonçalves, YMH; Senac, C; Fuchs, PFJ; Hünenberger, PH; Horta, BAC
Influence of the treatment of non-bonded interactions on thermodynamic and transport properties of pure liquids calculated using the 2016H66 force field. J. Chem. Theory Comput. 15, 1806–1826, 2019.

Ramos, MC; Horta, VAC; Horta, BAC
Molecular dynamics simulations of PAMAM and PPI dendrimers using the GROMOS-compatible 2016H66 forcefield. J. Chem. Inf. Model. 59, 1444-1457, 2019.

2018

da Silva, GC; Cardozo, TM; Amarante, GW; Abreu, CRA; Horta, BAC
Solvent effects on the decarboxylation of trichloroacetic acid: insights from ab initio molecular dynamics simulations. Phys. Chem. Chem. Phys. 20, 21988-21998, 2018.

Melo, IL; Lube, LM; Terra, WS; Fernandes, C; Matos, CRR; Franco, RWA; Resende, JALC; Valente, DCA; Horta, BAC; Cardozo, TM; Horn Jr., A
Experimental and theoretical studies of a greener catalytic system for cyclohexane chlorination promoted by trichloroisocyanuric acid and a copper(II) compound. Appl. Catal. A 562, 150-158, 2018.

Póvoa, RCBL; Koshiyama, AS; Dias, DM; Souza, PL; Horta, BAC
Multi-modal optimization by multi-gene genetic programming. IEEE Congress on Evolutionary Computation, 2172-2179, 2018. [conference paper]

Sueges, NS; Rodriguez, AA; Diederichs, CC; de Souza, SP; Leão, RAC; Miranda, LSM; Horta, BAC; Pedraza, SF; de Carvalho, OV; Pais, KC; Terra, JHC; de Souza, ROMA
Continuous-flow synthesis of (R)-propylene carbonate: an important intermediate in the synthesis of tenofovir. Eur. J. Org. Chem. 2018, 2931-2938, 2018.

da Silva, RP; Ambrósio, MFS; Piovesan, LA; Freitas, MCR; de Aguiar, DLM; Horta, BAC; Epprecht, E; San Gil, RAS; Visentin, LC
New solvatomorphic form of dexamethasone acetate monohydrate (DEX-II). J. Pharm. Sci. 107, 672-681, 2018.

2017

Senac, C; Urbach, W; Kurtisovski, E; Hünenberger, PH; Horta, BAC; Taulier, N; Fuchs, PFJ
Simulating bilayers of nonionic CiEj surfactants with the GROMOS-compatible 2016H66 force field. Langmuir 33, 10225-10238, 2017.

Oliveira, ERA; de Alencastro, RB; Horta, BAC
New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. J. Comput. Aided Mol. Des. 31, 1009-1019, 2017.

Tavara, EGM; Vellasco, MMBR; Horta, BAC; Custodio, FL
Feature importance calculation and protein quality assessment on the decoy discrimination problem. 2017 International Joint Conference on Neural Networks (IJCNN) [conference paper]

David, KS; Oliveira, ERA; Horta, BAC; Valente, AP; de Paula, VS
Insights into chemokine ligand 2 – chemokine receptor 2 molecular recognition: a step forward towards anti-chemotactic agents. Biochemistry 56, 3197-3210, 2017 .

Oliveira, ER; Mohana-Borges, R; de Alencastro, RB; Horta, BAC
The flavivirus capsid protein: Structure, function and perspectives towards drug design. Virus Res. 227, 115-123, 2017.

Pereira, AA; Pereira, AS; de Mello, AC; Carpanez, AG; Horta, BAC; Amarante, GW
Methylsulfenylation of electrophilic carbons: Reaction development, scope, and mechanism. Eur. J. Org. Chem. 2017, 1578-1582, 2017.

 

2016

Oliveira, ERA; de Alencastro, RB; Horta, BAC
The mechanism by which P250L mutation impairs flavivirus-NS1 dimerization: an investigation based on molecular dynamics simulations. Eur. Biophys. J. 45, 573-580, 2016.

Horta, BAC; Merz, PT; Fuchs, PFJ; Dolenc, J; Riniker, S; Hünenberger, PH
A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set. J. Chem. Theory Comput. 12, 3825-3850, 2016.

Collazos, SO; Gonçalves, YMH; Horta, BAC; Picciani, PHS; Louro, SRW; Oliveira Jr, ON; Pimentel, AS
Langmuir films and Mechanical Properties of Polyethyleneglycol Fatty Acid Esters at the Air-Water Interface. Coll. Surf. A 498, 50-57, 2016.

 

2015

Bellini, RG; Guimarães, AP; Pacheco, MAC; Dias, DM; Furtado, VR; de Alencastro, RB; Horta, BAC
Association of the anti-tuberculosis drug rifampicin with a PAMAM dendrimer. J. Mol. Graph. Model. 60, 34-42, 2015.

de Miranda, AS; Simon, RC; Grischek, B; de Paula, GC; Horta, BAC; de Miranda, LSM; Kroutil, W; Kappe, CO; de Souza, ROMA
Chiral chlorohydrins from the biocatalyzed reduction of chloroketones: chiral building blocks for antiretroviral drugs. ChemCatChem 7, 984-992, 2015.

Laner, M; Horta, BAC; Hünenberger, PH
Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J. Mol. Graph. Model. 55, 48-64, 2015.

2014

Laner, M; Horta, BAC; Hünenberger, PH
Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations. Eur. Biophys. J. Biophys. Lett. 43, 517-544, 2014.

Campomanes, P; Neri, M; Horta, BAC; Roehrig, UF; Vanni, S; Tavernelli, I; Röthlisberger, U
Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle. J. Am. Chem. Soc. 136, 3842-3851, 2014.

Rusu, VH; Horta, VAH; Horta, BAC; Lins, RD; Baron R
MDWiZ: A platform for the automated translation of molecular dynamics simulations. J. Mol. Graph. Model. 48, 80, 2014.

2012

Fuchs, PFJ; Hansen, HS; Hünenberger, PH; Horta, BAC
A GROMOS parameter set for vicinal diether functions: properties of polyethyleneoxide and polyethyleneglycol. J. Chem. Theory Comput. 8, 3943, 2012.

Horta, BAC; Lin, Z; Huang, W; Riniker, S; van Gunsteren, WF; Hünenberger, PH
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two β-peptides in methanol. J. Comput. Chem. 33, 1907, 2012.

Riniker, S; Horta, BAC; Thijssen, B; Gupta, S; van Gunsteren, WF; Hünenberger, PH
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: A molecular dynamics simulation study. ChemPhysChem 13, 1182-1190, 2012.

Kunz, APE; Allison, J.; Geerke, DP; Horta, BAC; Hünenberger, PH; Riniker, S; Schmid, N; van Gunsteren, WF
New functionalities in the GROMOS biomolecular simulation software. J. Comput. Chem. 33, 340, 2012.

2011

Eichenberger, AP; Allison, J.; Dolenc, J; Geerke, DP; Horta, BAC; Meier, K; Oostenbrink, C; Schmid, N; Steiner, D; Wang, D; van Gunsteren, WF
The GROMOS++ software for the analysis of biomolecular simulation trajectories. J. Chem. Theory Comput. 7, 3379, 2011.

Hoelz, LVB; Ribeiro, AAST; Bernardi, R; Horta, BAC; Araújo, JQ; Albuquerque, MG; Silva, JFM; Pascutti, P; Alencastro, RB
The role of helices 5 and 6 on the human β1-adrenoceptor activation mechanism. Mol. Sim. 38, 236, 2011.

Hoelz, LVB; Bernardi, R; Horta, BAC; Araújo, JQ; Albuquerque, MG; Silva, JFM; Pascutti, P; Alencastro, RB
Dynamical behaviour of the human β1-adrenoceptor under agonist binding. Mol. Sim. 37, 907, 2011.

Horta, BAC; Hünenberger, PH
Enantiomeric segregation in the gel phase of lipid bilayers. J. Am. Chem. Soc. 133, 8464, 2011.

Horta, BAC; Alencastro, RB
Structural and dynamic effects of changing the pattern of disulfide bonds in the vascular endothelial growth factor. Rev. Virtual Quim. 3, 37, 2011.

Horta, BAC; Fuchs, PFJ; van Gunsteren, WF; Hünenberger, PH
New interaction parameters for oxygen compounds in the GROMOS force field: improved pure-liquid and solvation properties for alcohols, ethers, aldehydes, ketones, carboxylic acids and esters. J. Chem. Theory Comput. 7, 1016, 2011.

2010

Horta, BAC; Perić-Hassler, L; Hünenberger, PH
Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: A comparative molecular dynamics study. J. Mol. Graph. Model. 29, 331, 2010.

Horta, BAC; De Vries, AH; Hünenberger, PH
Simulating the transition between gel and liquid-crystal phases of lipid bilayers: dependence of the transition temperature on the hydration level. J. Chem. Theory. Comput. 6, 2488, 2010.

Hoelz, LVB; Horta, BAC; Araújo, JQ; Albuquerque, MG, Alencastro, RB; Silva, JFM
Quantitative structure-activity relationship of antioxidant phenolic compounds. J. Chem. Pharm. Res. 2, 291, 2010.

2009

Horta, BAC; Sodero, ACR; Alencastro, RB
Investigating the differential activation of vascular endothelial growth factor (VEGF) receptors. J. Mol. Graph. Model. 28, 287, 2009.

Silva, BV; Horta, BAC; Alencastro, RB; Pinto, AC
Kinase protein: structural features and chemical inhibitors. Química Nova, 32, 453, 2009.

2008

Horta, BAC; Cirino, JJV; Alencastro, R B
On the Structure, interactions, and dynamics of bound vascular endothelial growth factor. J. Mol. Graph. Model. 26, 1091, 2008.

Ribeiro, AAST; Horta, BAC; Alencastro, RB
MKTOP: A program for automatic construction of molecular topologies. J. Braz. Chem. Soc. 19, 1433, 2008.

Miranda, J; Silva, CJ; Moura, L.; Herbst, M; Horta, BAC; Alencastro, RB; Albuquerque, M
Deamination process in the formation of a copper(II) complex with glutamic acid and a new ligand derived from guanidinoacetic acid: Synthesis, characterization, and molecular modeling studies. Polyhedron, 27, 2386, 2008.

Horta, BAC; Cirino, JJV; Alencastro, RB
Dynamical behavior of the vascular endothelial growth factor: Biological implications. Proteins, 67, 517, 2007. With erratum: Proteins, 70, 307, 2008.

2007

Chou, TF; Tikh, IB; Horta, BAC; Gosh, B; Alencastro, RB; Wagner, CR
Engineered monomeric human histidine triad nucleotide binding protein 1 (hHint1) hydrolyzes fluorogenic acyl adenylate and LysRS generated lysyl-adenylate. J. Biol. Chem. 282, 15137, 2007.

2005

Esteves, PM; Araujo, CL; Horta, BAC; Alvarez, LJ; Zicovich-Wilson, CM; Ramirez-Solis, A
The isobutylene-isobutane alkylation process in liquid HF revisited. J. Phys. Chem. B, 109, 12946, 2005.

 

Development and Application of Molecular
Models and Computational Methods 

Team

 

Prof. Bruno A. C. Horta
MSSM - Group Leader
Yan M. H. Gonçalves
MSSM - PhD Student
Guilherme C. Q. da Silva
MSSM - PhD Student
Mayk C. Ramos
MSSM - Master Student

 

André Borges Farias
MSSM - PhD Student
Luciano M. da Silva Junior
MSSM - Undergraduate Student
Douglas Viana Ferreira
MSSM - Undergraduate Student
Maria Clara Solla Etchevers Silva
MSSM - Undergraduate Student

 

Igor de Andrade A. de Almeida
MSSM - Undergraduate Student

 

 

Former Group Members

Rogério C. B. L. Póvoa
MSSM - PhD

Dr. Edson R. A. Oliveira
MSSM - Postdoc

 

 

Contact Us

Instituto de Química UFRJ
Av. Athos da Silveira Ramos, 149
Centro de Tecnologia, Bloco A, Sala 609
21941-909, Cidade Universitária
Rio de Janeiro – RJ, Brazil
+55-21-3938-7132