# Computational Systems Biology and Bioinformatics

## Welcome to the SCL Computational Systems Biology and Bioinformatics Research Interest Group Page!

This is a special research interest group under SCL that aims to understand the properties and behavior of complex biological systems, in terms of its individual (molecular) components and how they interact at different levels of the organization. Specifically, we are interested in the study of efficient extraction, storage, analysis and integration of important biological information from these systems through utilization of different computational approaches, such as modeling, data mining, machine learning and visualization, to give meaningful insights from these biological data, and for us to provide answers to pressing problems in computational systems biology.

## Research Projects

Currently, there are active research areas being tackled by the group, which include the following:

### 1. Construction and Analysis of Potential Energy Hypersurfaces for Protein Structure Prediction through Quantum Chemical Calculations

*John Justine Villar, M.Sc., Adrian Roy Valdez, PPhD, in collaboration with David Setiadi, PhD (University of Toronto, Canada), Amador Muriel, Ph.D. (The City University of New York, USA) and Imre Csizmadia, PhD (University of Miskolc, Hungary)*

This study aims to construct precise potential energy surfaces (PES) of different amino acids through *ab initio* calculations to provide insights on the potential energy hypersurface given an amino acid sequence. We intend to compare our findings to results from well-known force fields, among others. Furthermore, the relationship between polypeptide PES and amino acid PES are also explored.

*Jerome Cary Beltran, Catalina Montes, John Justine Villar, PhD and Adrian Roy Valdez, PhD*

This research aims to incorporate biological information into purely graph-based clustering methods to more precisely predict relevant protein complexes from protein-protein interaction networks (PPIN). The resulting algorithm will be compared to existing PPIN frameworks, in terms of the number of complexes correctly predicted from gold standard datasets, and other performance metrics.

**Second Prize, 2015 UP College of Engineering Undergraduate Project Competition*

*Gerald Roy Campañano, Francis Jonathan Lopez, Rowel Ventura, John Justine Villar, PhD and Adrian Roy Valdez, PhD*

This project aims to predict the final conformation of a protein by sampling possible conformations through an off-lattice model. This also provides a parallel implementation of the simulated annealing algorithm for conformational energy minimization. The results were applied to several proteins from Protein Data Bank, where minimum energy values and number of hydrogen bonds were compared.

## Selected Research Publications

Villar JJS, Negm L, Ragyánszki A, Setiadi DH, Valdez ARL, Viskolcz B, Csizmadia IG. **A Prelude to Building Mathematical Models for Polypeptide Folding: Analysis on the Conformational Potential Energy Hypersurface Cross-Sections of N-Acetyl-Glycyl-Glycine-N'-Methylamide****. ***Canadian Journal of Chemistry*, 96(10), 2018. 912-921.

Villar JJS, Valdez ARL, Setiadi DH, Viskolcz B, Csizmadia IG, Rágyanszki A. **An Improved Two-Rotor Function for Conformational Potential Energy Surfaces of 20 Amino Acid Diamides*****. ***Canadian Journal of Chemistry* 96(1), 2018. 58-71.

Villar JJS, Valdez ARL, Setiadi DH, Fiser B, Viskolcz B, Csizmadia IG, Rágyanszki A. **Dimension Reduction in Conformational Analysis: A Two-Rotor Mathematical Model of Amino Acid Diamide Conformational Potential Energy Surface**. *Canadian Journal of Chemistry *95(8), 2017. 830-836.

Beltran JCB, Montes CA, **V**illar JJ**S **and Valdez ARL.** A Hybrid Method for Detecting Protein Complexes in Weighted Protein-Protein Interaction Networks. ***Philippine Science Letters *10(1), 2017. 50-57.

Villar JJ, Rágyanszki AR, Valdez AR, Setiadi D, Viskolcz B and Csizmadia IG. **Mathematical Representation of 20 Amino Acid Diamide Relaxed Conformational Potential Energy Surfaces.*** Proc. 6th Visegrad Symposium on Structural Systems Biology 2016, Warsaw, Poland, 2016.*

Campañano GR, Lopez FJ, Ventura R, Villar, JJ and Valdez AR. **Off-lattice Protein Structure Prediction on 3D Hydrophobic-Polar Side-Chain Model using Parallel Simulated Annealing. ***Proceedings of the Mathematical Society of the Philippines Annual Convention 2016, Cebu City, Philippines, 2016.*

Villar JJ, Rágyanszki AR, Valdez AR, Setiadi D, Viskolcz B and Csizmadia IG. **Analysis of Models for Analytical Fitting of Conformational Potential Energy Surfaces. ***Proc. Kemometria és Molekulamodellezés Munkabizottsága-QSAR és Modellezési Szakcsoportja Szimposia (KeMoMo-QSAR 2016), Miskolc, Hungary, 2016.*

Beltran JC, Montes C, Villar JJ, Soriano J and Valdez AR.** On Incorporating Core-Attachment Scheme for Protein Complex Detection on Weighted Protein-Protein Interaction Networks. ***Proceedings of the 2015 Mathematical Society of the Philippines Annual Convention, Laoag City, Philippines, 2015.*

Gozum RP, Mendoza KM, Villar JJ, Soriano J and Valdez AR. **On Protein Structure Prediction using the Hydrophoic-Polar Model on a Tetrahedral Lattice. ***Proceedings of the 2015 Mathematical Society of the Philippines Annual Convention, Laoag City, Philippines, 2015.*

Beltran JC, Montes C, Villar JJ, Soriano J and Valdez AR.** A Hybrid Method for Detecting Protein Complexes in Weighted Protein-Protein Interaction Networks. ***Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.*

Gozum RP, Mendoza KM, Villar JJ, Soriano J and Valdez AR. **A Branch-and-Bound Method for the 3D HP Protein Folding Model over a Tetrahedral Lattice. ***Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.*

Soriano J, Valdez AR and Fontanilla IK.** Discrimination of Class Aves Families Using Codon Counts From Unaligned COI Sequences.** *Proceedings of the 8th Research Workshop on Modeling, Simulation and Scientific Computing in the Philippines (MODEL 2015), Manila, Philippines, 2015.*

Soriano J, Sapasap R, Chua T, Santi N, Fontanilla I and Valdez AR. **DNA Barcoding of Class Aves Species Using Codon Counts with Artificial Neural Network**. *International Conference of Artificial Intelligence in Computer Science. Langkawi, Malaysia, 2013.*

Soriano J, Rondon R, Meneses A, Cardenas M, Lim-Yap S and Valdez AR. **Creating Functional Groups for Palanan Forest Dynamics Plot using Linear Discriminant Analysis**. *International Conference of Artificial Intelligence in Computer Science. Langkawi, Malaysia, 2013.*

* Villar JJS and Valdez ARL. **A Process Algebra Model of Interleukin-2 Trafficking in Hematopoeitic Cells****. ***Theory and Practice of Computation*. PICT Vol 7, Springer Japan, 2013.

* *

**Recipient, 2013 International Publication Award (Book Chapter), Office of the Vice President for Academic Affairs, University of the Philippines System*

For queries, comments, and suggestions on matters with regards to the group, please contact Dr. Adrian Roy Valdez at alvaldez@up.edu.ph.