2024年12月9日 · User-provided CCD + custom ligand codes. This enables specifying ligands not in CCD, while also supporting specification of covalent bonds to other entities and backup reference coordinates for when RDKit fails to generate a conformer. This offers the most flexibility, but also requires careful attention to get all of the details right.

2024年11月27日 · I'm looking to model a protein sequence including some modifications: N-glycosylation of some Asn residues. I tried to input this by using CCD code "NAG" or "ASN_NAG" and the specified residue number, but this did not correctly attach a N-glycan. What is the correct input for N-glycan modifications of the protein sequence input?

The Chemical Component Model data file contains the matching chemical structures in the Chemical Component Dictionary and the Cambridge Structural Database (CSD) archive.

Ligands can include molecules such as ATP, ADP, and ions like Mg2+ or Zn2+. For other ligands, use the 3-letter CCD code. Example:

2024年12月8日 · I noticed an unexpected behavior when specifying a ligand with userCCD: the job would fail if the "ccdCodes" field is a list of str, for example: "ccdCodes": ["Lig-1"]. However, it runs fine if a simple str is provided: "ccdCodes": "Lig-1".

As previously announced, the PDBx/mmCIF dictionary has been extended to enhance PCM and PTM annotation. This includes new PDBx/mmCIF categories and items as follows: In the Chemical Component Definition (CCD) files: A new item in the chem_comp category: chem_comp.pdbx_pcm, stating whether the CCD is a known PCM/PTM.

2014年12月2日 · Summary: The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules.

2022年4月28日 · This function generates Central Composite Designs (CCD) with coded levels for a given number of input factors (v). The CCD constitute combinations of factorial points, axial points and center points.

2024年11月19日 · Predict biomolecular structures using AlphaFold, Boltz-1 and Chai-1. Click on 'Add protein', 'Add DNA', 'Add RNA' or 'Add ligand' to enter the corresponding sequences, CCD codes or ligand SMILES strings.

2021年1月28日 · As per Krishna Veni et al (2020), environment-sensitive Eudragit coated solid lipid nanoparticles can be prepared using a central composite design (CCD) model [9].