VMD: Visual molecular dynamics

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

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The Protein Data Bank

Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

/pdf/features-and-development-of-coot-5al5bhwkg1.pdf

Features and development of Coot.

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

/pdf/the-pfam-protein-families-database-3t3lguk949.pdf

The Pfam protein families database

The Protein Data Bank: a computer-based archival file for macromolecular structures.

The Protein Data Bank: a computer-based archival file for macromolecular structures

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1977.tb11885.x

The Protein Data Bank. A computer-based archival file for macromolecular structures.

Vancomycin, a broad-spectrum antibiotic, inhibits the growth of cell walls by complex formation with peptides terminating in D-alanyl-D-alanine. The structure of vancomycin was determined by X-ray analysis of the degradation product CDP-I. A model of the complex is proposed based on this study and spectroscopic data.

Structure of vancomycin and its complex with acetyl- D -alanyl- D -alanine

DETAILS of the molecular architecture of double helical ribonucleic acids at atomic resolution have recently become available from single crystal X-ray diffraction studies of dinucleotides composed of complementary bases1–3. No similar studies have been published for deoxynucleotides. We report here the structure of the deoxytetranucleotide d-pApTpApT (5′-P-adenylyl-(3′-5′)-thymidylyl-(3′-5′)-adenylyl-(3′-5′)-thymidine) (I) at a resolution of 1.0 A. This is the first tetranucleotide whose structure has been elucidated by X-ray diffraction. The work is part of an investigation of protein–nucleic acid interactions using single-crystal studies of small model compounds. d-pApTpApT was chosen as one of the first compounds to be examined because there is evidence that poly(dA–dT) has unusual binding properties and that A.T-rich regions in certain DNAs have specific biological roles4–7. We hope that these investigations will provide information about the influence of specific base pairs and sequences on the fine details of the DNA structures, and thus aid the understanding of the selective recognition of nucleotide sequences of the DNA double helix by proteins.

O. Kennard

Papers

The Protein Data Bank: a computer-based archival file for macromolecular structures.

The Protein Data Bank: a computer-based archival file for macromolecular structures

The Protein Data Bank. A computer-based archival file for macromolecular structures.

Structure of vancomycin and its complex with acetyl- D -alanyl- D -alanine

DNA double helical fragment at atomic resolution.