# Molecular Structure Checking using BioExcel Building Blocks (biobb) *** This tutorial aims to illustrate the process of **checking** a **molecular structure** before using it as an input for a **Molecular Dynamics** simulation. The workflow uses the **BioExcel Building Blocks library (biobb)**. The particular structure used is the crystal structure of **human Adenylate Kinase 1A (AK1A)**, in complex with the **AP5A inhibitor** (PDB code [1Z83](https://www.rcsb.org/structure/1z83)). **Structure checking** is a key step before setting up a protein system for **simulations**. A number of **common issues** found in structures at **Protein Data Bank** may compromise the success of the **simulation**, or may suggest that longer **equilibration** procedures are necessary. The **workflow** shows how to: - Run **basic manipulations on structures** (selection of models, chains, alternative locations - Detect and fix **amide assignments** and **wrong chiralities** - Detect and fix **protein backbone** issues (missing fragments, and atoms, capping) - Detect and fix **missing side-chain atoms** - **Add hydrogen atoms** according to several criteria - Detect and classify **atomic clashes** - Detect possible **disulfide bonds (SS)** An implementation of this workflow in a **web-based Graphical User Interface (GUI)** can be found in the [https://mmb.irbbarcelona.org/biobb-wfs/](https://mmb.irbbarcelona.org/biobb-wfs/) server (see [https://mmb.irbbarcelona.org/biobb-wfs/help/create/structure#check](https://mmb.irbbarcelona.org/biobb-wfs/help/create/structure#check)). *** ## Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. 