Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate in catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature in macromolecules can make them difficult to model and refine, and a substantial portion of metal ions in the PDB are misidentified or poorly refined. CheckMyMetal (CMM) is a validation tool that has gained widespread acceptance as an essential tool for researchers working on metal-macromolecule complexes. CMM can be used during structure determination or to validate metal binding sites in structural models within the PDB. The functionalities of CMM have recently been greatly enhanced and provide researchers with additional information that can guide modeling decisions. The new version of CMM shows metals in the context of electron density maps and allows for onthe-fly refinement of metal binding sites. The improvements should increase the reproducibility of biomedical research.

Molecular modeling is an excellent tool for studying biological systems on the atomic scale. Depending on objects, which may be proteins, nucleic acids, or lipids, different force fields are recommended. The phospholipid bilayers constitute an example, in which behavior is extensively studied using molecular dynamics simulations due to limitations of experimental methods. The reliability of the results is strongly dependent on an appropriate description of these compounds. There are some deficiencies in the parametrization of intra- and intermolecular interactions that result in incorrect reproduction of phospholipid bilayer properties known from experimental studies, such as temperatures of phase transitions. Refinement of the force field parameters of nonbonded interactions present in the studied system is required to close these discrepancies. Such parameters as partial charges and torsional potential coefficients are crucial in this issue and not obtainable from experimental studies. This work presents a new fitting procedure for torsional coefficients that employs linear algebra theory and compares it with the Monte Carlo method. The proposed algebraic approach can be applied to any considered molecular system. In the manuscript, it is presented on the example of dimethyl phosphoric acid molecule. The advantages of our method encompass finding an optimal solution, the lack of additional parameters required by the algorithm, and significantly shorter computational time. Additionally, we indicate the importance of proper assignment of the partial charges.

The overall quality of the experimentally determined structures contained in the PDB is exceptionally high, mainly due to the continuous improvement of model building and structural validation programs. Improving reproducibility on a large scale requires expanding the concept of validation in structural biology and all other disciplines to include a broader framework that encompasses the entire project. A successful approach to science requires diligent attention to detail and a focus on the future. An earnest commitment to data availability and reuse is essential for scientific progress, be that by human minds or artificial intelligence. 1．Introduction The Protein Data Bank(PDB) 1) was formed over 50 years ago and initially contained only seven macromolecular structures. The PDB founders realized that access to macromolecular models is essential for crystallographers, students, and researchers who might use structural information for their research. Initially, every deposit contained only the coordinates of the atoms. Even then, every new structure was carefully checked to see whether the 3-D model agreed with known chemical and physical properties. Since 2007, every submission to the PDB has had two additional components: 1)information about the sample (crystal in X-ray crystallography) , a rough description of the experimental setup, and other metadata(header) , and 2)intensity amplitudes(usually called structure factors) of all diffraction spots measured during the experiment. The deposit header also contains additional information like authors, connections to other databases, software used to determine the structure, etc. These three components allow for calculating the electron density map and checking whether the macromolecule model, including ligands, nucleic acids, and solvent, agrees with experimental data. This checking procedure is called validation of the macromolecular model and was usually performed by the experimenter at the end of the structure determination process. The PDB also routinely performs validation on all deposited structures. 2) Moreover, scientists who find disagreement between their experiments and PDB deposits can perform validations for themselves. Sometimes their validation triggers a re-refinement and leads to the deposition of a new, improved model to the PDB. 3)Occasionally, new biomedical interpretations arise from improved structural models. 4)

CheckMyMetal is a server used to validate the metal binding sites of macromolecular structures. An easy-to-use interface allows the evaluation of structures in the PDB or uploaded by the user. The new version incorporates electron density maps, which expands the number of parameters used for validation. The structure and maps are now displayed using the NGL viewer and provide a more informative and intuitive experience. One of the most important new features is the ability to conduct a fast refinement of the vicinity around alternate metal candidates. CheckMyMetal guides the metal selection process in two ways. First, it evaluates the substitution of several metals in the current environment, re-scores the binding sites, and displays a ranked list of candidate metals. Second, the researcher is alerted to potential metals from the crystallization conditions when they are available. The refined metal binding site containing the newly selected metals can be downloaded. CheckMyMetal is available at cmm.minorlab.org.