What do you mean by "bumps"?

Molecular docking usually predicts the pose of certain compounds in a target protein pocket. For good docking calculation, it is expected that the predicted protein-ligand complex should contain no intermolecular steric clash (or bump). For binding energy, molecular dynamics simulation is therefore suggested, considering MM-PBSA or MM-GBSA binding energy calculation.

Intermolecular steric clashes imply unfavorable nonpolar contribution to the binding free energy. The size and/or shape of the binding site might not be suitable for the clashing compound. Small clashes may disappear if the complex is let to relax (e.g., using molecular dynamics simulations).

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Dear colleagues,

Department of Pharmacy, Universitas Muhammadiyah Palangkaraya openly inviting researchers with expertise in the field of Molecular Docking to join the new journal that will be released in early 2021, both as an editorial board and as peer-reviewers.

We will call this journal "Journal of Molecular Docking" or "J. Mol. Docking", with a very specific aim and scope, namely various research in the field of science and health using Molecular Docking as its main method.

Currently we are still preparing the journaling platform with OJS 3.1.1.2 and will start collecting articles as soon as the editorial board and peer-reviewer members are gathered. The link for this new journal is http://journal.umpalangkaraya.ac.id/index.php/jmd.

It should be noted that this position is voluntary, so all editors and reviewers will not receive any rewards in the form of funds. However, we will provide a certificate of appreciation for each manuscript handled, both as an editor and reviewer.

The target of this new journal is to be indexable by DOAJ after the first year and indexed by Scopus and/or ESCI WoS after the fifth year.

For this reason, we expect the willingness and participation of Molecular Docking researchers to be directly involved in the development of this new journal so that later it can become a publication benchmark for research with the molecular docking method.

Once again, we are grateful for the participation of all researchers and hope for their support to be able to create and grow this new journal.

Best regards,

Mohammad Rizki Fadhil Pratama

Assistant Professor of Medicinal Chemistry

Universitas Muhammadiyah Palangkaraya

http://orcid.org/0000-0002-0727-4392

Is there any way to eliminate intermolecular steric clash (or bump) while performing molecular docking?