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Research and Development

physics
informatics
technology
engineering
medicine

Discoveries Technology

We are a multidisciplinary group of scientists interested in understanding the fundamental Structure-Dynamics-Function relationship observed in natural biomolecules and the role their diversity plays in the mechanisms of complex biological processes through a robust Theoretical-Computational-Experimental approach. The biological models we use to study Biomolecular Diversity are viruses, antibiotics, proteins, and lipid membranes.
We use an integrative approach, leveraging methods and techniques from Molecular Biophysics, Multi-Scale Molecular Modeling, Molecular Dynamics, Bioinformatics, Molecular Biology, Structural Biology, Mechanics of Biomaterials, Biotechnology and Genetic Engineering, Information Systems and Software Development.

25

Scientific Peer-Reviewed Publications

25

Students Graduated

7

Awards Received

3

Funded Mega-Projects

11

Software Developments

500

plus Citations

Research Publications

Scopus ResearchGate ResearcherID ORCID
CV Google Scholar PubFacts LinkedIn

Most Cited

  1. (2009) VIPERdb2: An enhanced and web API enabled relational database for structural virology.
    Nucleic Acids Research . 37:D436-D442
    CV 10.1093/nar/gkn840 IF: 9.202
  2. (2003) A comparative study of the hydration of Na+ and K+ with refined polarizable model potentials.
    Journal of Chemical Physics . 118:7062-7073
    CV 10.1063/1.1559673 IF: 2.894
  3. (2005) Evidence for a mechanism by which w-3 polyunsaturated lipids may affect membrane protein function.
    Biochemistry . 44:10164-10169
    CV 10.1021/bi050822e IF: 2.876
2018

  1. CapsidMesh: atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties.
    International Journal for Numerical Methods in Biomedical Engineering . e2991
    Featured on the Journal's Cover: CV
    CV 10.1002/cnm.2991 IF: 2.192
  2. HTMol: full-stack solution for remote access, visualization, and analysis of Molecular Dynamics trajectory data.
    Journal of Computer-Aided Molecular Design 32:869-876
    CV 10.1007/s10822-018-0141-y IF: 2.356
  3. VIPERdb: A Tool for Virus Research.
    Annual Review of Virology . In press
    CV 10.1146/annurev-virology-092917-043405 IF: 5.345
2017

  1. A Multi-Phase Solvation Model for Biological Membranes: Molecular Action Mechanism of Amphotericin B.
    Journal of Chemical Theory and Computation . 13:3388–3397
    CV 10.1021/acs.jctc.7b00337 IF: 5.301
  2. Plant-based chimeric HPV-virus-like particles bearing amyloid-β epitopes elicit antibodies able to recognize amyloid plaques in APP-tg mouse and Alzheimer´s disease brains.
    Inflammopharmacology . in press
    CV 10.1007/s10787-017-0408-2 IF: 2.590
  3. Porcine circovirus type 2 protective epitope densely carried by chimeric papaya ringspot virus-like particles expressed in E. coli as a cost-effective vaccine manufacture alternative.
    Biotechnology and Applied Biochemistry . 64:406-414
    CV 10.1002/bab.1491 IF: 1.429
  4. Evolution of substrate specificity in a retained enzyme driven by gene loss.
    eLife . 6:e22679
    CV 10.7554/eLife.22679 IF: 8.282
2016

  1. Structure based sequence analysis of viral and cellular protein assemblies.
    Journal of Structural Biology . 196:299-308
    CV 10.1016/j.jsb.2016.07.013 IF: 2.570
  2. An Amphotericin B derivative equally potent to Amphotericin B and with increased safety.
    PloS One . 11:e0162171
    CV 10.1371/journal.pone.0162171 IF: 3.057
  3. Antagonism or synergism between Papaya ringspot virus and Papaya mosaic virus in Carica papaya is determined by their order of infection.
    Virology . 489:179-191
    CV 10.1016/j.virol.2015.11.026 IF: 3.200
2015

  1. Highly efficient strategy for the heterologous expression and purification of soluble Cowpea chlorotic mottle virus capsid protein and in vitro pH-dependent assembly of virus-like particles.
    Journal of Virological Methods . 225:23-29
    CV 10.1016/j.jviromet.2015.08.023 IF: 1.508
  2. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google maps.
    Journal of Structural Biology . 190:47-55
    CV 10.1016/j.jsb.2015.02.003 IF: 2.570
  3. Insights into the evolution of enzyme substrate promiscuity after the discovery of (beta alpha)8 isomerase evolutionary intermediates from a diverse metagenome.
    BMC Evolutionary Biology . 15:107-121
    CV 10.1186/s12862-015-0378-1 IF: 3.406
2014-1997

10 published scientific papers

Technology Development

Methods, Protocols, Modeling, Visualization, and Analysis Tools for the Study of BioMolecular Diversity, Structural Biology and Biological BigData

VIPERdb
Structural Virology

VIPERdb Science Gateway

Global Repository of Structural Virology: Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The capsid has the fundamental functions to protect and transport the viral genome, and recognize the host cell. VIPERdb is a database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools.

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Structural Virology

CapsidMaps & S-score

CapsidMaps is an interactive analysis and visualization tool. It facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity S-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application.

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CapsidMesh
Structural Virology

CapsidMesh

Descriptions of the capsid macromolecular complex have been proposed at different scales of approximation in the past, however, little is known about the physical properties of the capsid. CapsidMesh is a methodology to generate a structured volumetric mesh of icosahedral viral capsids based on their atomic information. The CapsidMesh models are suitable for numerical simulations and analysis of a physical process. We have used CapsidMesh to simulate the capsid nanoindentation of several viruses previously characterized by Atomic Force Microscopy experiments. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.

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HTMoL
Structural Bioinformatics

HTMoL

Next-generation Molecular Dynamics Web Visualization: HTMoL is a light-weight full-stack plugin-free application to display the three-dimensional structure and dynamics of biomolecules on any web browser. HTMoL can be used as a graphical interface to access MD data located at a high performance computing cluster where simulations are generated, or as supplementary documentation for scientific research publications as a way to readily share MD results.

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MMPSM
Molecular Modeling

MMPSM: Membrane Multi-Phase Solvation Model

We use a thermodynamic approach in which we represent the biological membrane by a multiphase solvation model with atomic detail and calculate the free energy of transferring a drug molecule between phases with different dielectric properties.

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HTMgene
Bioinformatics

HTMgene

AI-based 2D analysis of 'omics' derived data (e.g. microarrays, differential gene expression, etc.)
"The English-language neologism omics informally refers to a field of study in biology ending in -omics, such as genomics, proteomics or metabolomics. The related suffix -ome is used to address the objects of study of such fields, such as the genome, proteome or metabolome respectively. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms." Read more.

Coming soon
MDdb
Structural Bioinformatics

MDdb

The Molecular Dynamics database.
"Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules, and is thus a type of N-body simulation. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are calculated using interatomic potentials or molecular mechanics force fields. The method was originally developed within the field of theoretical physics in the late 1950s but is applied today mostly in chemical physics, materials science and the modelling of biomolecules." Read more.

Coming soon

Group Members

Alumni

Postdoctoral

  1. José M. Falcón González (2015)
  2. Mónica N. Jiménez García (2014)
  3. Alcione García González (2010)

Ph. D.

  1. José L. Alonzo Velázquez (2017)
  2. Daniel J. Montiel García (2016)

Masters

  1. Omar I. Lara Ramirez (2016)
  2. Angélica A. Serrano Rubio (2015)
  3. Armando Díaz Valle (2014)
  4. Victor Villa Moreno (2013)
  5. Guillermo Amaro Rico (2013)
  6. Gabriela Chávez Calvillo (2012)

Diploma

  1. Emmanuel Quijas Valades (2017)
  2. Julio C. González Vázquez (2017)
  3. Eduardo González Zavala (2017)
  4. José Cabello Zavala (2016)
  5. Eliot G. Cruz Ponce (2016)
  6. Leonardo Alvarez Rivera (2015)
  7. Francisco J. Becerra Toledo (2015)
  8. Adan Vega Ramírez (2015)
  9. Joel Chacón Castillo (2014)
  10. Oscar Ornelas Alvarado (2014)
  11. Miguel A. Ochoa Montes (2014)
  12. Ramiro Ramos Meléndes (2014)
  13. Francisco Aguilar Salas (2014)
  14. Adrián Benavides Rosales (2014)

Research Assistant

  1. J. Julian Santoyo Flores (2016)
  2. Gabriel Jiménez Domínguez (2016)
  3. Victor Villa Moreno (2014)
  4. Mariana Andrade Medina (2013)

Research Team

Ph. D.

  1. Domingo Jiménez López (2022)
  2. Mariana Andrade Medina (2021)

Masters

  1. Alejandra G. Valdéz Lara (2019)
  2. Raúl A. Galván Juárez (2019)
  3. Aldo A. Pérez Montoya (2019)
  4. A. Yarely de la Rosa González (2019)

Research Assistant

  1. Claudia Cruz Belli (since 2018)

Development Team

Tech. Assistant

  1. Nelly B. Santoyo Rivera (since 2011)
  2. José Cabello Zavala (since 2017)
  3. Leonardo Alvarez Rivera (since 2017)

Collaborations

UK

  1. Dr. Ali Tavassoli, University of Southampton

USA

  1. Dr. Charles Brooks III, University of Michigan
  2. Dr. Vijay S. Reddy, The Scripps Research Institute
  3. Dr. Chris Henry, Argonne National Laboratory
  4. Dr. Scott Feller, Wabash College

CINVESTAV

  1. Dra. Laura Silva Rosales, Departamento de Ingeniería Genética
  2. Dr. Miguel Gómez Lim, Departamento de Ingeniería Genética
  3. Dr. Amilcar Meneses Viveros, Departamento de Computación
  4. Dr. Francisco Barona Gómez, Unidad de Genómica Avanzada

UNAM

  1. Dr. Iván Ortega Blake, Instituto de Ciencias Físicas
  2. Dr. Rubén Paul Gaytán Colin, Unidad de Síntesis y Secuenciación de ADN, Instituto de Biotecnología

CIMAT

  1. Dr. Salvador Botello Rionda, Departamento de Computación
  2. Dr. Rafael Herrera Guzmán, Departamento de Matemáticas Básicas

IPN

  1. Dr. José M. Falcón González, Unidad Profesional Interdisciplinaria de Ingeniería

CIATEJ

  1. Dr. Abel Gutiérrez Ortega, Unidad de Biotecnología Médica y Farmacéutica

UANL

  1. Dra. Alcione García González, Fisicoquímica de Interfases, Facultad de Ciencias Químicas

UAEM

  1. Dr. Carlos Amero Tello, Laboratorio de Bioquímica y Resonancia Magnética Nuclear, Centro de Investigaciones Químicas

bmd

Mauricio Carrillo-Tripp, Ph. D.

Principal Investigator
Unidad Monterrey
CINVESTAV
México

e-mail

mauricio.carrillo@cinvestav.mx

phone

+52 811 156 1740 ext 4520