RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of: These data can be explored in context of external annotations providing a structural view of biology. 3D visualization for PDB structures and ligand binding sites.

Protein Data Bank (PDB) format is a standard for files containing atomic coordinates. It is used for structures in the Protein Data Bank and is read and written by many programs. While this short description will suffice for many users, those in need of …

2024年4月16日 · Fatal error:Atom OCT1 in residue PRO 440 was not found in rtp entry PRO with 16 atoms while sorting atoms. 请问可以直接把PDB文件中的1OCT和2OCT改成.rtp文件中的命名即O吗？

2024年10月5日 · In order to explore the structure and analyze molecular interactions in atomic detail, the locations of each atom in the PDB must be uniquely assigned. Various identifiers are used to specifically indicate one atom or groups of atoms.

2023年3月31日 · 在pdb文件中，atom模块是记录蛋白质分子中原子坐标信息的模块，每一行代表一个原子的坐标信息。 如下图所示是pdb文件的部分内容： 第一列：记录原子的标识号；第二列：原子序号；第三列：原子名称；第四列：残基名称；第五列：链ID；第六列：残基序号 ...

The primary information stored in the PDB archive consists of coordinate files that list the atoms in each structure and their 3D location in space, along with summary information about the structure, sequence, and experiment.

As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to …

PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format. PDB intends to verify the coordinates against the experimental structure factor data in the when available. Details on this will be forthcoming.

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides ( Pure & Appl. Chem., 70, 117-142, 1998 ) with the exception of the well established convention for C ...

This server is written for automated repair of protein structure file in PDB or mmCIF format and assignment of secondary structure elements using the repaired file. As our understanding of proteins increase so will the capability of the server