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Post-doctoral Research Fellowship (BIPD) (Reference REQUIMTE 2023-12)

6 Feb 2023

Job Information

REQUIMTE - Rede de Quimica e Tecnologia
Research Field
Chemistry » Computational chemistry
Researcher Profile
First Stage Researcher (R1)
Application Deadline
Type of Contract
Job Status
Is the job funded through the EU Research Framework Programme?
Not funded by an EU programme
Is the Job related to staff position within a Research Infrastructure?

Offer Description

A Post-doctoral Research Fellowship (BIPD) (Reference REQUIMTE 2023-12) at the Research Unit on Applied Molecular Biosciences (UCIBIO) - UIDB/04378/2020, with the financial support of the FCT/ MCTES through national funds is available at REQUIMTE.


Main research field: Chemistry


Admission requirements:

The prospective candidates must hold a PhD in Chemistry, Biochemistry, Medicinal Chemistry, Bioinformatics, Cheminformatics or similar scientific areas, obtained in the previous three years to the date of submission of the application, and have proven experience in Computer-Aided Drug Discovery and Molecular Dynamics Simulations. A good programming background (e.g. Python) and experience in developing pipeline workflows integrating different in silico methods in computer-aided drug discovery projects is highly desirable (RDKit, KNIME, etc), as well as a good knowledge of High-Performance Computing.


The host institution where the research work was developed that led to the attribution of the candidate's doctoral degree must be different from Research Unit on Applied Molecular Biosciences (UCIBIO).

In case the doctorate degree was awarded by a foreign higher education institution, it must comply with the provisions of Decree-Law no. 341/2007 of October 12th, and all formalities established therein must be complied until the signature of the contract.


Workplan: The main goal is to develop and optimize workflows for integrating different in silico methods for application in computer-aided drug discovery projects, including:


(1) acquisition of compounds data from public databases;

(2) filtering datasets by ADME and other properties;

(3) creation and optimization of their 3D structures;

(4) preparation of appropriate 3D libraries for structural-based virtual screening;

(5) selection and preparation of 3D structures of the target or multiple-targets;

(6) incorporation of different independent docking tools and scoring functions in the workflow;

(7) creation of target-specific validation sets and automated target-specific protocol optimization and its application to the desired 3D compound databases;

(8) selection of top hits, force field parameterization of the compounds and molecular dynamics simulations of the corresponding target-ligand complexes (with AMBER, CHARMM or GROMACS);

(9) analysis of molecular dynamics simulation properties and free energy calculations (FEP, TI, MM-PBSA).

Applicable Legislation: The grant is awarded under the Research Fellowship Holder    Statute, approved by Law nº 40/2004, of August 18th, and updated by Law decree 123/2019, of August 28th, and the Regulation for Studentships and Fellowships of the Fundação para a Ciência e a Tecnologia, I.P.:


Work Place: The work will be conducted at FMUP in the Biomolecular Simulations Research Lab (BioSIM), under the supervision of Sérgio Filipe Sousa. BioSIM is a research group that works in bridging the gap between theory and experiment applying and developing state-of-the-art computational tools focusing on Drug Discovery, Enzymatic Catalysis and Molecular Recognition. It combines QM/MM Methods, Quantum Mechanics, Molecular Dynamics, Docking, Virtual Screening, and Free Energy Perturbation methods, always in close linking with experiment. It has also been involved in the development of several software applications and scientific databases that have been made available to the scientific community. More information can be found on the group’s website (



Duration of the fellowship: The fellowship will have duration of 6 months, potentially renewable for additional periods of 6 months, up to 36 months, expected to start on March 2023.


Monthly stipend: Monthly stipend is €1686 according to the stipends established by FCT, I.P. in Portugal ( Payment will be made by bank transfer on a monthly basis. The successful candidate will also be entitled to the reimbursement of Social Security payments (Seguro Social Voluntário) and work insurance.


Selection criteria: Selection of candidates will be performed according to the following criteria: i) 20%, overall scientific coherence of the CV, including diversity and quality of scientific indicators, including relevant published peer-reviewed articles in the specific areas of the announcement;

ii) 25%, experience in the creation of data flows or pipelines in computer-aided drug discovery with software like KNIME or similar alternatives;

iii) 25%, demonstrated experience in creation of 3D databases, cheminformatics applications, and docking/virtual screening;

iv) 20%, demonstrated experience in molecular dynamics simulations of biomolecular systems with classical force fields (AMBER, CHARMM, GROMACS, etc);

v) 10%, experience in high-performance computing, cluster-management and code-optimization.

In the case of admitted candidates whose evaluation does not differ by more than 10% of the classification obtained by the best positioned candidate, the jury will interview these candidates, with the interview accounting for 50% of the final classification.

Please note that the jury reserves the right not to award the current scholarship if the results of the evaluation of candidates and its adequacy to the project's objectives is not satisfactory, i.e., candidates with a final classification lower than 50%.

Composition of the Selection Jury: Dr. Sérgio Filipe Sousa (president of the selection jury), Professor Dr. Pedro Jorge Araújo Alves da Silva (vowel), Professor Dr. André Melo (vowel) and Dr. Nuno Manuel Ferreira de Sousa de Azevedo Cerqueira (substitute vowel).


Publicity and communication of results: The ranking of applications will be published at a visible and public area of REQUIMTE facilities, and all candidates will be informed by email about the result of their application.



The call for applications is open between 07/02/2023 and 20/02/2023.

The applications are formalized at the electronic address, containing in the subject the reference to which the candidate is applying (Reference REQUIMTE 2023-12) with following documents in a digital form, in PDF format and will include Curriculum vitae, Motivation letter, Qualifications Certificate and other documents deemed relevant.


More information:   



Research Field
Education Level
PhD or equivalent

Additional Information

Work Location(s)

Number of offers available

Where to apply



Praça Coronel Pacheco, nº 15 6º andar
Postal Code