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Research Club on Bioinformatics

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Research Club on Bioinformatics

  

Card session 4 Pathfinder Club
  • The Club
  • Members
  • Future perspectives
  • Club Meetings

 

The Bioinformatics Research Club TGHN LAC - BioinFar aims to consolidate theoretical and practical knowledge in chemistry, structural biochemistry and computational simulation, articulated to the biological context of research, as a foundation for mastering and critically applying advanced methodologies of molecular docking and molecular dynamics in scientific investigations of regional and global impact. The Club is a multidisciplinary environment focused on knowledge exchange, scientific development and practical application of bioinformatics in different areas of life sciences and technology.

The club also stands out for its collaborative and formative character, comprising undergraduate students, postgraduate students, biomedical professionals, pharmacists, researchers and professors. Thus, the Club promotes a space where beginners can learn from experienced researchers, whilst established professionals have the opportunity to share knowledge, discuss projects and develop new scientific partnerships. This interaction between different academic and professional profiles makes the environment more dynamic, enriching both the learning and scientific output of participants.

About the Bioinformatics Research Club:

  • Mode: hybrid.
  • Language: Portuguese
  • Frequency: fortnightly
  • Date of first meeting: 6 February 2026

Members

The group has 17 participants, comprising 9 women and 8 men. Most are from the state of Ceará, whilst one participant is from Campinas, São Paulo. Among the members are professionals and students from the fields of Biomedicine, Pharmacy, Biological Sciences, Systems Analysis and Development, as well as researchers working directly with topics such as bacterial resistance, antibody development, microbiology, molecular biology and computational modelling applied to health sciences.

The presence of individuals with expertise in technology and programming strengthens the group's capacity to deal with computational tools, omic data analysis, construction of bioinformatics pipelines and interpretation of large volumes of biological data. At the same time, participants with laboratory and clinical experience bring an applied and translational perspective to discussions, bridging bioinformatics with the real demands of biomedical and pharmaceutical research.

 

Jaime Ribeiro Filho – Coordinator. Fiocruz Cearā | Orcid

Ernesto Caffarena – Mentor and consultant in bioinformatics. Researcher PROCC, Fiocruz | Orcid

Ketlen Christine Ohse – Collaborator and organiser. Postdoctoral researcher Fiocruz Cearā | Orcid

Ana Beatriz Oliveira Bezerra. University Centre Doctor Leão Sampaio; Juazeiro do Norte-CE | Orcid

Antônio Cícero Viana de Lima Neto. Christus University-Unichristus; Fortaleza-CE | Orcid

Cicera Laura Roque Paulo. Regional University of Cariri – URCA; Crato-CE | Orcid

Francisco Isac Soares Leite. Regional University of Cariri-URCA; Pombal-PB | Orcid

Inara Bianca Pascoal Marques. University Centre Doctor Leão Sampaio; Juazeiro do Norte-CE

Joey Ramone Ferreira Fonseca. State University of Campinas (UNICAMP); Campinas-SP | Orcid

Juliana Ramos de Oliveira. Fiocruz Cearā; Eusébio-CE | Orcid

Kamilla Bezerra Cabral. Regional University of Cariri-URCA; Crato-CE | Orcid

Lara Saraiva da Silva. Regional University of Cariri-URCA; Crato-CE | Orcid

Maick Douglas Fernandes Amaral. State University of Ceará; Limoeiro do Norte-CE | Orcid

Maria Bianca Aguiar Feitosa. University Centre Doctor Leão Sampaio-UNILEAO; Caririaçu-CE

Maria Clara Fernandes de Lima. Regional University of Cariri-URCA; Juazeiro do Norte-CE

Ray Silva de Almeida. University Centre Doctor Leão Sampaio | Orcid

Rayna Lelaiah Rodrigues Melo. University Centre Doctor Leão Sampaio; Missão Velha-CE | Orcid

Samuel Andrade de Araújo. Federal Institute of Paraíba; Marizópolis-PB

Silvio Caetano Alves Junior. Fiocruz Bahia; Crato-CE | Orcid

Thiago Mesquita Cândido. Federal University of Ceará; Fortaleza-CE | Orcid

Future Perspectives

The future perspectives of the Bioinformatics Club are focused on the training and technical development of its members, especially considering that much of the group is still in the process of education and building experience in the bioinformatics field. One of the main objectives is to promote collective learning, allowing all participants to develop theoretical and practical knowledge on computational tools applied to scientific research.

Among the group's goals, the development of members' capacity to conduct and understand molecular docking analysis stands out, from theoretical fundamentals to results interpretation, contributing to applications in areas such as drug development, bacterial resistance, protein-ligand interaction and computational structural biology.

Beyond technical training, the club also seeks to encourage collaborative scientific output, stimulating the development and publication of research articles, as well as participation in congresses, symposiums and academic events representing the group. Thus, it is expected to strengthen both the academic training and scientific and professional experience of its members, consolidating the Bioinformatics Club as a space for learning, collaboration and scientific growth.

Club Meetings

Meeting 1 (30/05/2026) – Introduction to Linux for Bioinformatics

Objectives

  • Understand what Linux is
  • Difference between Linux, Windows and macOS
  • Why Linux dominates bioinformatics

Content

  • Terminal
  • Directory structure
  • Basic navigation

Commands

pwd, ls, cd, mkdir, rm, cp, mv

Practical activity

  • Create project folders
  • Organise docking files

Meeting 2 (13/06/2026) – Linux Applied to Bioinformatics

Content

  • Permissions
  • Software installation
  • Environment variables
  • File manipulation

Commands

chmod, grep, cat, head, tail, find

Practical application

  • Search for .pdb files
  • Organise results
  • Automate small tasks

Meeting 3 (27/06/2026) – Introduction to Structural Bioinformatics and Docking

Objectives

  • What is structural bioinformatics
  • What is molecular docking
  • Difference between docking, molecular dynamics and QSAR
  • General workflow of a project

Tools presented

PyMol, AutoDock, Avogadro, GAMESS

Discussions

  • Pharmacological applications
  • Drug discovery
  • Bacterial resistance
  • Limitations of docking

Meeting 4 (11/07/2026) – Functional Groups of Organic Chemistry

Content

  • Hydroxyl
  • Carbonyl
  • Carboxyl
  • Amines
  • Amides
  • Thiols
  • Aromatics
  • Heterocycles

Focus on docking

  • How functional groups influence polarity
  • Interaction
  • Affinity
  • Protonation

Activity

Identification of functional groups in real drugs

Meeting 5 (25/07/2026) – Amino Acids: Structure and Classification

Content

  • Polar and nonpolar amino acids
  • Positively and negatively charged
  • Aromatics
  • Hydrophobic

Application

  • How residues interact with ligands
  • Active sites

Tool

Visualisation in PyMol

Meeting 6 (08/08/2026) – Protein Structure

Content

  • Primary structure
  • Secondary
  • Tertiary
  • Quaternary

Important concepts

  • Folding
  • Domains
  • Structural motifs

Application

  • Recognition of catalytic pockets
  • Protein flexibility

Meeting 7 (22/08/2026) – Intermolecular Interactions I

Content

  • Hydrogen bonds
  • Hydrophobic interactions
  • van der Waals

Practical application

  • How to interpret poses in docking

Exercise

Visual analysis of protein-ligand complexes

Meeting 8 (05/09/2026) – Intermolecular Interactions II

Content

  • Pi stacking
  • Cation-pi
  • Salt bridges

Discussion

  • Energetic importance
  • Complex stability

Tool

PyMol

Meeting 9 (19/09/2026) – Force Field and Molecular Energy

Content

  • Concept of force field
  • Potential energy
  • Energy minimisation

Force fields

AMBER, CHARMM, GROMOS

Critical discussion

Limitations of classical models

Meeting 10 (03/10/2026) – Geometry Optimisation

Content

  • Classical mechanics vs quantum mechanics
  • Structural minimisation

Programmes

Avogadro, GAMESS

Practical activity

Optimisation of a simple ligand

Meeting 11 (17/10/2026) – Introduction to Python for Bioinformatics

Content

  • Variables
  • Loops
  • File manipulation

Libraries

Pandas, RDKit

Application

Automation of docking analysis

Meeting 12 (31/10/2026) – Introduction to PyMol

Content

  • Load proteins
  • Structural representations
  • Identification of residues

Application

  • Visualisation of active sites
  • Distance measurements

Meeting 13 (07/11/2026) – Ligand Preparation

Content

  • 2D → 3D structures
  • Protonation
  • Minimisation

Tools

Avogadro, OpenBabel

Important discussion

Common errors that invalidate docking

Meeting 14 (21/11/2026) – Protein Preparation

Content

  • Water removal
  • Structural correction
  • Addition of hydrogens

Tool

AutoDock Tools

Meeting 15 (05/12/2026) – Grid Box and Active Site

Content

  • What is a grid box
  • How to define coordinates
  • Blind docking vs focused docking

Tool

PyMol + AutoDock

Meeting 16 (06/02/2027) – Introduction to AutoDock 4

Content

  • .pdbqt files
  • Conversion of atomic types
  • Docking configuration

Discussion

  • Genetic algorithm
  • Affinity score

Meeting 17 (20/02/2027) – Execution of Molecular Docking

Objectives

  • Generate poses
  • Interpret energy
  • Assess RMSD

Practical activity

Run complete docking

Meeting 18 (06/03/2027) – Interpretation of Results

Content

  • Binding affinity
  • Relevant interactions
  • False positives

Critical discussion

Why low energy does not always mean a better compound

Meeting 19 (20/03/2027) – Automation and Data Analysis

Content

  • Simple scripts
  • Results organisation
  • Pose filtering

Libraries

Pandas, RDKit

Meeting 20 (03/04/2027) – Limitations of Molecular Docking

Advanced discussion

  • Protein flexibility
  • Solvent
  • Protonation
  • Force field dependency

Objective

Develop scientific critical thinking

Meeting 21 (17/04/2027) – Participants' Seminars

Presentations from participants

Each member presents:

  • A research article
  • A molecular target
  • A workflow
  • A critical analysis
Card session 4 Pathfinder Club
  • The Club
  • Members
  • Future perspectives
  • Club Meetings

 

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