Savíns Puertas Martín

PhD in Informatics

Contact

savinspm@ual.es
+34 950214394
Personal website
Building CITE III. Room 1.13.
Carr. Sacramento, s/n,
04120 La Cañada, Almería

Social Networks

References

PhD Full Prof. G. Ester Martín Garzón

Head of Supercomputing-Algorithm Research Group.
University of Almería

gmartin@ual.es
PhD Prof. Horacio Pérez-Sánchez

Head of Bioinformatics and High Performance Computing
Universidad Católica San Antonio de Murcia (UCAM)

hperez@ucam.edu/span>
PhD Full Prof. Pilar Martínez Ortigosa

Master and Thesis Supervisor
University of Almería

ortigosa@ual.es
PhD Prof. Juana López Redondo

Master and Thesis Supervisor
University of Almería

jlredondo@ual.es

Hobbies

Photography (2.8k followers)
Chess (Candidate Master Title)
More than 200 trophies

Savíns Puertas Martín

PhD in Informatics

Profile

Savíns Puertas Martín is currently on a two-year research stay (2022-20224) in the Chemoinformatics group at the University of Sheffield, United Kingdom.
He finished his degree in Computer Engineering at the University of Almeria in June 2015, receiving the prizes for the best record of the promotion and the best final project. In September of the same year, he started the Master's degree in Computer Engineering at the same university and obtained a Collaboration Scholarship in which he began working in the area of drug development. During his second year of Master, he started a PhD in Computer Science funded by a 4-year FPU grant from the Spanish Ministry, also in Almeria. In June 2017, he finished the Master's degree, obtaining the best record and the best Master's thesis. He finished his PhD in October 2020 with the highest qualification, cum laude, and international mention. His research has focused on the design and development of different drug development techniques. Specifically, a technique called Virtual Screening, which is normally used as one of the first stages in the drug development process, reducing the number of compounds to be analysed later, saving time and money. Among its developments is the OptiPharm software, for which he has registered its intellectual property (RTA-94-18). OptiPharm software has been sued by several universities and companies in different countries. It is currently being used for two projects: one related to COVID-19 with international commercial interests and another with a European company in which effects have been found that could be relevant for the treatment of certain medical conditions and which is still in the experimental phase. In addition to following this line, Savins worked for a year on a radiotherapy project and, more specifically, on the improvement and automation of the planning of intensity-modulated radiotherapy (IMRT). He is currently in Sheffield (UK) on a two-year research stay on virtual screening and molecular flexibility. His teaching activity has been related to Computer Architecture and Technology, High-Performance Computing and Computer Networks.

Work Experiance

Post-doctoral Researcher 01.02.2022-now
Chemoinformatics research group. Information School. University of Sheffield, United Kingdom
  • working on Virtual Screening problems and molecular flexibility.
Post-doctoral Researcher 01.02.2021-31.01.2022
Supercomputing-Algorithm Research Group. Dept. of Informatics, University of Almería
  • working on the project High Performance Computing for Optimizing Intensity Modulated Radiation Therapy Schedules
Pre-doctoral Researcher. National Competitive Scholarship FPU (Formación de Profesorado Universitario (University Teacher Training)).01.10.2016-30.09.2020
Supercomputing-Algorithm Research Group. Dept. of Informatics, University of Almería
Research Labor Staff 01.06.2016-30.09.2016
Supercomputing-Algorithm Research Group. Dept. of Informatics, University of Almería

Awards and Achievements

VII Research Awards Scientific Computer Society of Spain (SCIE) - BBVA Foundation 2022. 2022
22th November
  • Prize: 5.000 €
Third prize in Your PhD Thesis in Three Minutes competition. 2021
Jornadas Sarteco 22-24 September
Official Accreditation.2021
National Agency for Quality Assessment and Accreditation
  • Assistant Doctor Professor
  • Private University Professor
  • Hired Doctor Professor
FPU Scholarship 2016-2020
Spanish Ministry of Education, Culture and Sport
  • The FPU scholarship provides  nancial support for awardees to complete an o cial PhD program and to carry out research and teaching activities, in any discipline, by signing a predoctoral contract.
  • Code: FPU15/02912.
Best Final project award in Informatics Master 2018
EPS-FCCEE - University of Almería
Best academic record award in Informatics Master 2018
University of Almeria. Informatics Master.
Collaboration grant with the Department of Informatics of the University of Almeria, 2016
Spanish Ministry of Education, Culture and Sport
Best  nal project award in Informatics Degree2015
EPS-FCCEE - University of Almería
Best academic record award in Informatics Degree 2015
University of Almeria. Informatics Degree.

Education

PhD in Informatics 2016-2020
University of Almería
  • Score: Cum laude (maximum score). International Mention.
  • Thesis title: High Performance Computing for Optimization Problem Solving in Bioinformatics.
Master in Informatics2015-2017
University of Almería
  • Average score: 9.79 out 10.
  • Final master project title: Solving optimization problems in the pharmaceutical industry through evolutionary algorithms.
Degree in Informatics 2011-2015
University of Almería
  • Average score: 9.55 out 10.
  • Final degree project title: a voice interaction system for handling mashup interfaces.

Research Publication

Journal Articles
  1. M. R. Ferrández, S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “A two-layer mono-objective algorithm based on guided optimization to reduce the computational cost in virtual screening,” Scientific Reports, vol. 12, no. 1, p. 12 769, Dec. 2022 , issn: 2045-2322. doi: 10.1038/s41598-022-16913-w.  [Online]. Available: https://doi.org/10.1038/s41598-022-16913-w
  2. S. Puertas-Martín, J. L. Redondo, M. R. Ferrández, H. Pérez-Sánchez, and P. M. Ortigosa, “MultiPharm-DT: A Multi-Objective Decision Tool for Ligand-Based Virtual Screening Problems,” Informatica, pp. 1–26, Dec. 2021, issn: 0868-4952. doi: 10.15388/21-INFOR469. [Online]. Available: https://doi.org/10.15388/21-INFOR469
  3. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Optimizing Electrostatic Similarity for Virtual Screening: A New Methodology,” Informatica, pp. 1–19, Jul. 2020, issn: 0868-4952. doi: 10.15388/20-INFOR424. [Online]. Available: https://informatica.vu.lt/doi/10.15388/20INFOR424.
  4. S. Puertas-Martín, A. J. Banegas-Luna, M. Paredes-Ramos, J. L. Redondo, P. M. Ortigosa, O. O. Brovarets’, and H. Pérez-Sánchez, “Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts?” Expert Opinion on Drug Discovery, vol. 15, no. 9, pp. 981–986, 2020, issn: 1746045X. doi: 10.1080/17460441.2020.1758664. [Online]. Available: https://doi.org/10.1080/ 17460441.2020.1758664.
  5. S. Puertas-Martín, J. L. Redondo, P. M. Ortigosa, and H. Pérez-Sánchez, “OptiPharm: An evolutionary algorithm to compare shape similarity,” Scientific Reports, vol. 9, no. 1, p. 1398, Dec. 2019, issn: 2045-2322. doi: 10.1038/s41598-018-37908-6. [Online]. Available: http://www.nature.com/articles/s41598-018-37908-6.
  6. A. J. Banegas-Luna, J. P. Cerón-Carrasco, S. Puertas-Martín, and H. Pérez-Sánchez, “BRUSELAS: HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases,” Journal of Chemical Information and Modeling, vol. 59, no. 6, pp. 2805–2817, Jun. 2019, issn: 1549-9596. doi: 10.1021/acs.jcim.9b00279. [Online]. Available: https://pubs.acs.org/doi/101021/acs.jcim.9b00279. .
  7. M. R. Ferrández, S. Puertas-Martín, J. L. Redondo, B. Ivorra, A. M. Ramos, and P. M. Ortigosa, “Highperformance computing for the optimization of high-pressure thermal treatments in food industry,” The Journal of Supercomputing, vol. 75, no. 3, pp. 1187–1202, Mar. 2019, issn: 0920-8542. doi: 10.1007/s11227018-2351-4. [Online]. Available: http://link.springer.com/10.1007/s11227-018-2351-4.
International Conferences
  1. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, V. J. Gillet, and P. M. Ortigosa, “Optimization based on atom-pair properties in flexible ligands by optipharm,” in XV. Workshop on Global Optimization, Uni- versity of Szeged, Szeged, Hungary, Sep. 2022.
  2. J. J. Moreno, S. Puertas-Martín, J. L. Redondo, L. G. Casado, P. M. Ortigosa, and E. M. Garzón, “A new hybrid optimization algorithm to combine physical and biological criteria to compute imrt planning,” in 19th Workshop on Advances in Continuous Optimization, University Nova de Lisboa, Lisbon, Portugal, Jul. 2022.
  3. J. J. Moreno, S. Puertas-Martín, J. L. Redondo, P. M. Ortigosa, and E. M. Garzón, “Acceleration of the tuning of eud model for imrt planning on multigpu clusters,” in 22th International Conference Computa- tional and Mathematical Methods in Science and Engineering, University of Cadiz, Rota, Spain, Jul. 2022.
  4. S. Puertas-Martín, J. L. Redondo, A. J. Banegas-Luna, E. M. Garzón, H. Pérez-Sánchez, V. J. Gillet, and P. M. Ortigosa, “Virtual screening based on electrostatic similarity and flexible ligands,” in The 22nd In- ternational Conference on Computational Science and Its Applications, University of Malaga, Malaga, Spain, Jul. 2022.
  5. S. Puertas-Martín, J. L. Redondo, V. J. Gillet, H. Pérez-Sánchez, and P. M. Ortigosa, “Optimization method for maximizing the similarity in flexible molecules,” in 19th Workshop on Advances in Contin- uous Optimization, University Nova de Lisboa, Lisbon, Portugal, Jul. 2022.
  6. S. Puertas-Martín, J. J. Moreno, J. L. Redondo, P. M. Ortigosa, A. Zawadzka, J. Miroforidis, I. Kaliszewski, and E. M. Garzón, “New multiobjective strategies to optimize constrained eud radiotherapy models,” in 26th International Conference on Multiple Criteria Decision Making, University of Portsmouth, Portsmouth, United Kingdom, Jun. 2022.
  7. S. Puertas-Martín, J. L. Redondo, E. M. Garzón, H. Pérez-Sánchez, and P. M. Ortigosa, “Increasing the accuracy of optipharm’s virtual screening predictions by implementing molecular flexibility,” 9th International Work-Conference on Bioinformatics and Biomedical Engineering, University of Granada, Gran Canaria, Spain, Jun. 2022
  8. S. Puertas-Martín, J. J. Moreno, J. L. Redondo, P. M. Ortigosa, and E. M. Garzón, “Optimizing eud model parameters in radiotherapy planning,” in The 7th Int’l Conf on Health Informatics and Medical Systems, American Council on Science and Education, Las Vegas, USA, Jul. 2021.
  9. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Optimization of molecular descriptors using memetic algorithms,” in 18th Workshop on Advances in Continuous Optimization, EurOpt2021, Ecole Nationale de l’Aviation Civile, Toulouse, France, Jul. 2021.
  10. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Maximizing the electrostatic similarity in drug discovery through evolutionary algorithms,” in 8th International Work-Conference on Bioinformatics and Biomedical Engineering, University of Granada, Granada, Spain, Sep. 2020.
  11. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Virtual screening in electrostatic potential using an evolutionary algorithm,” in Proceedings of META18: 7th International Conference on Metaheuristics and Nature Inspired Computing, Université de Lille, Marrakech, Morocco, Oct. 2018, pp. 207–209.
  12. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Multi-objective evolutionary algorithm for evaluation of shape and electrostatic similarity,” in Proceedings of LeGO 2018 - Int. Workshop on Global Optimization. AIP Conference Proceedings, Leiden University, vol. 1, Sep. 2018, pp. 1–4, isbn: 9780735417984. doi: 10.1063/1.5089986. [Online]. Available: http://aip.scitation.org/doi/abs/10.1063/1.5089986.
  13. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Optimizing electrostatic similarity using a global evolutionary algorithm,” in Proceedings of 6th EUROPT Workshop on Advances in Continuous Optimization, University of Almería, Almería, Spain, Jul. 2018.
  14. S. Puertas-Martín, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Virtual screening in molecular shape by using an evolutionary algorithm,” in Proceedings OLA’2018 International Workshop on Optimization and Learning: Challenges and Applications, Université de Lille, Alicante, Spain, Feb. 2018, pp. 63–64.
  15. M. R. Ferrández, S. Puertas-Martín, J. L. Redondo, B. Ivorra, R. A. M, and O. P. M, “High-performance computing for optimizing high-pressure thermal treatments in food processing,” in Proceedings of the 17th International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2017, University of Cadiz, Alicante, Spain, Jul. 2017, pp. 862–869, isbn: 978-84-617-8694-7.
  16. S. Puertas-Martín, M. R. Ferrández, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Enhancing molecular shape comparison by a parallel global evolutionary algorithm,” in Proceedings of the 17th International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2017, University of Cadiz, Rota, Spain, Jul. 2017, pp. 1722–1728, isbn: 978-84-617-8694-7.
  17. S. Puertas-Martín, H. den-Haan, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Enhancing molecular shape comparison by a global evolutionary algorithm,” in 4th International Work-Conference on Bioinformatics and Biomedical Engineering, University of Granada, Granada, Spain, 2016.
  18. S. Puertas-Martín, J. L. Redondo, H. den-Haan, H. Pérez-Sánchez, and P. M. Ortigosa, “Multi-objective based scoring function for ligand based virtual screening,” in Proceedings of the XIII Global Optimization Workshop, University of Minho, Braga, Portugal, 2016, isbn: 978-989-20-6764-3.
Educational Conferences
  1. J. J. Moreno, S. Puertas-Martín, F. Orts, N. C. Cruz, J. L. Redondo, E. Garzón, and O. P. M., “On simulating an arm processor for teaching computer structure,” in 12th annual International Conference of Education, Research and Innovation (ICERI 2019), Seville, Spain, Dec. 2019.
  2. F. Orts, N. C. Cruz, S. Puertas-Martín, M. Ruiz-Ferrández, J. J. Moreno, C. Medina-López, P. M. Ortigosa, V. Ruíz, L. Casado, J. M. Salmerón, J. L. Redondo, G. E. Garzón, G. Ortega, and R. Villegas, “Learning quantum computation through simple examples,” in 11th International Conference of Education, Research and Innovation (ICERI 2019), Seville, Spain, Dec. 2019.
  3. F. Orts, N. C. Cruz, S. Puertas-Martín, M. Ruiz-Ferrández, J. J. Moreno, C. Medina-López, P. M. Ortigosa, V. Ruíz, L. Casado, J. M. Salmerón, J. L. Redondo, G. E. Garzón, G. Ortega, and R. Villegas, “Learning quantum computation through simple examples,” in 11th International Conference of Education, Research and Innovation (ICERI 2019), Seville, Spain, Dec. 2019.
  4. N. C. Cruz, M. R. Ferrández, E. M. Garzón, J. M. García Salmerón, L. González Casado, V. González Ruiz, C. Medina-López, J. J. Moreno, G. Ortega López, P. M. Ortigosa, F. J. Orts, S. Puertas-Martín, J. L. Redondo, J. F. Sanjuan Estrada, and T. Santamaría López, “Simulación de un procesador arm para la enseñanza de estructura de computadores. poster,” in Jornadas de Innovación Docente y Experiencias Profesionales en la Universidad de Almería. Curso 2019-20, Vicerrectorado de Enseñanzas Oficiales y Formación Continua y por la Coordinación de Gobierno e Interacción con la Sociedad y las Empresas de la Universidad de Almería, Almería, Spain, Sep. 2019.
  5. S. Puertas-Martín, J. J. Moreno, F. J. Orts, N. C. Cruz, J. L. Redondo, E. M. Garzón, and P. M. Ortigosa, “Simulación de un procesador arm para la enseñanza de estructura de computadores,” in Actas de las Jornadas SARTECO 2019, Cáceres, Spain, Sep. 2019, pp. 235–240, isbn: 978-84-09-12127-4.
  6. V. González-Ruiz, G. Ortega, E. Garzón, N. Calvo-Cruz, R. J. L., J. Salmerón, L. Casado, P. M. Ortigosa, C. Medina-López, J. J. Moreno, M. R. Ferrández, F. Orts, S. Puertas-Martín, and T. Santamaría-López, “Project-based learning: An experience,” in 11th International Conference on Education and New Learning Technologies (EDULEARN 2019), Palma, Spain, Jul. 2019.
  7. N. C. Cruz, M. R. Ferrández, E. M. Garzón, J. M. García Salmerón, L. González Casado, V. González Ruiz, C. Medina-López, J. J. Moreno, G. Ortega López, P. M. Ortigosa, F. J. Orts, S. Puertas-Martín, J. L. Redondo, J. F. Sanjuan Estrada, T. Santamaría López, and R. Villegas, “Recursos para el aprendizaje de computación cuántica en el grado de ingeniería informática. poster,” in Jornadas de Innovación Docente y Experiencias Profesionales en la Universidad de Almería. Curso 2018-19, Vicerrectorado de Enseñanzas Oficiales y Formación Continua y por la Coordinación de Gobierno e Interacción con la Sociedad y las Empresas de la Universidad de Almería, Almería, Spain, Sep. 2018.
National Conferences
  1. M. R. Ferrández, S. Puertas-Martín, J. L. Redondo, B. Ivorra, A. M. Ramos, and P. M. Ortigosa, “Computación de alto rendimiento para optimizar tratamientos térmicos de alta presión en la industria alimenticia,” in Avances en arquitectura y tecnología de computadores. Actas de las Jornadas SARTECO 2017, Málaga, Spain, Sep. 2017, pp. 119–122, isbn: 978-84-697-4835-0.
  2. S. Puertas-Martín, M. R. Ferrández, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Cribado virtual mediante un algoritmo evolutivo global paralelo,” in Actas de las Jornadas SARTECO 2017, Cácares, Spain, Sep. 2017, pp. 177–179, isbn: 978-84-697-4835-0.
  3. S. Puertas-Martín, M. R. Ferrández, J. L. Redondo, H. Pérez-Sánchez, and P. M. Ortigosa, “Algoritmo evolutivo global como herramienta de cribado virtual utilizando la forma molecular,” in III Jornadas Doctorales de la Universidad de Murcia, Murcia, Spain, May 2017, pp. 236–240, isbn: 978-84-608-9779-8.

Patents and Intellectual Properties

OPTIPHARM: an innovative evolutionary algorithm for virtual screening 2018
P. M. Ortigosa, J. L. Redondo, S. Puertas-Martín and H. Pérez-Sánchez.
  • University of Almería and Universidad Católica San Antonio de Murcia.
  • Application Number: 201899900606752. Register number: RTA-94-18.
  • Registration Date: 16/02/2018. Concession date: 09/08/2018.

Research Stays

Predoctoral Stay, 10.09.2018-10.12.2018
Centre for Logistics and Heuristic Optimization (CLHO), Kent Business School, University of Kent. Canterbury, CT2 7NZ, United Kingdom

Projects

Soluciones de Alto Rendimiento para retos actuales de la computación cientí ca (HPC4Sci) (High Performance Solutions for Today’s Scienti c Computing Challenges (HPC4Sci)). 01.01.2019 – 31.12.2021
National project.
  • Principal Research: Pilar Martínez Ortigosa and Gracia Ester Martín Garzón.
  • Number of researchers: 31.
  • Code: RTI2018-095993-B-100.
  • Funding: Spanish Ministry of Science and Innovation. National Program for Scienti c Research, Development and Technological Innovation
  • Total amount: 186.461,00 Euros
Computación de Altas Prestaciones para Optimizar Plani caciones de Radioterapia de IntensidadModulada (High Performance Computing to Optimize IntensityModulated Radiation Therapy Planning). 15.10.2019 – 14.10.2021
Regional project.
  • Principal Research: Ester Martín Garzón and Juana López Redondo.
  • Number of researchers: 14.
  • Code: UAL18-TIC-A020-B.
  • Funding: Junta de Andalucia, Fondos Feder UAL.
  • Total amount: 76.800,00 Euros.
Descubrimiento y optimización de compuestos bioactivos mediante técnicas avanzadas de química computacional (Discovery and optimization of bioactive compounds through advanced computational chemistry techniques).01.01.2019 – 31.12.2019
Regional project.
  • Principal Research: Horacio Emilio Pérez Sánchez.
  • Number of researchers: 12.
  • Code: 20988/PI/18.
  • Funding: Fundación Séneca.
  • Total amount: 62.000 Euros.
Metodologías computacionales para desafíos de la sociedad (Computational methodologies for societal challenges). 01.01.2016 – 31.12.2019
National project.
  • Principal Research: Leocadio González Casado and Pilar Martínez Ortigosa.
  • Number of researchers: 21.
  • Code: TIN2015-66680-C2-1-R.
  • Funding: Spanish Ministry of Economy and Competitiveness.
  • Total amount: 147.620 Euros.

Teaching Innovation Projects

Desarrollo de Recursos para motivar el estudio de la Ingeniería de Computadores (Development of Resources to motivate the study of Computer Engineering). 2019
Convocatoria de Grupos Docentes para la Creación de Materiales Didácticos en la Universidad de Almería. Bienio 2018 y 2019 (Call for Teaching Groups for the Creation of Didactic Materials at the University of Almeria. Biennial 2018 and 2019)
  • Funding: University of Almería.
  • Total amount: 800 Euros.
Desarrollo de Recursos para motivar el estudio de la Ingeniería de Computadores (Development of Resources to motivate the study of Computer Engineering).2018
Convocatoria de Grupos Docentes para la Creación de Materiales Didácticos en la Universidad de Almería. Bienio 2018 y 2019 (Call for Teaching Groups for the Creation of Didactic Materials at the University of Almeria. Biennial 2018 and 2019)
  • Funding: University of Almería.
  • Total amount: 800 Euros.

Teaching

Degree in Informatics 2019-2020
University of Almería, Spain
  • Network access technologies. Third year. 41 hours.
  • Peripherals and interfaces. Third year. 19 hours.
  • Quality Assurance System of the University of Almeria. Academic quality 4.72 out of 5.
Degree in Informatics 2018-2019
University of Almería, Spain
  • Structure and computer technology. First year. 38 hours
  • Network access technologies. Third year. 19 hours
  • Quality Assurance System of the University of Almeria. Academic quality 4.65 out of 5.
Degree in Informatics 2017-2018
University of Almería, Spain
  • Peripherals and interfaces. Third year. 19 hours.
  • Network access technologies. Third year. 19 hours.
  • Multi-processorss. Third year. 18 hours.
  • Structure and computer technology. First year. 2 hours
  • Quality Assurance System of the University of Almeria. Academic quality 4.82 out of 5.

Final Project Supervisor

Degree in Informatics, 2020-2021
University of Almería, Spain.
  • Co-supervisor in a Final Degree Project: Arti cial vision-based fall recognition (Reconocimiento de caídas con Visión Arti cial)
  • Co-supervisor in a Final Degree Project: Gesture control monitoring (Monitorización mediante control gestual)
Degree in Informatics, 2019-2020
University of Almería, Spain.
  • Co-supervisor in a Final Degree Project: SMARTFRIDGE: Recognition of Actions in a Refrigerator and Decision Making in a Smart Enviroment. Award: Best Final degree project.

Skills

Languages
C, C++, JAVA, Python, LATEX.
Parallel Programming Paradigms
MPI, PThreads.
Software applied to drug discovery
OpenEye’s Software (ROCS, EON, VIDA, OMEGA), OpenEye’s Toolkit, Pymol, Reflex3D, WEGA, OptiPharm