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.

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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/).

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The Pfam protein families database

An accurate single-crystal neutron diffraction analysis of the compound (H/sub 3/Pt/sub 2/(Ph/sub 2/PCH/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/)/sup +/(BPh/sub 4/)..sqrt.. is reported herein. The large crystal was obtained by the recrystallization of the compound from an acetone/ether mixture. The four coordinated platinum atom was found to have a normal square-planar geometry with interatomic angles close to ideal values. It was noted that the two bridging H atoms were marked by asymmetry of their position. The distances between the atoms are reported. The most accurate measurements of a terminal Pt-H bond distance to date is reported to be 1.610 A, while earlier measurements from x-ray diffraction were reported to be 1.527, 1.66, 1.78, and 1.98 A. 16 references, 1 figure.

Neutron diffraction analysis of (H/sub 3/Pt/sub 2/(Ph/sub 2/PCh/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/)/sup +/(BPh/sub 4/): an unusual example of an unsymmetrical (P/sub 2/Pt(. mu. -H)/sub 2/PtP/sub 2/H) core

We wish to report the first accurate neutron diffraction study of a transition metal structure with a triply bridging hydride ligand, the cluster HFeCo/sub 3/(CO)/sub 9/(P(OCH/sub 3/)/sub 3/)/sub 3/. The compound crystallizes in the space group P2/sub 1//c, Z = 4. The cell constants at 90 K are a = 15.957 (8) A, b = 10.611 (5) A/sub 9/ c = 18.383 (9) A, ..beta.. = 98.70 (2)/sup 0/. The structure was refined, based on the measured intensities of 8229 reflections; the final discrepancy factors for all reflections are R/sub F/sup 2// = 0.087, R/sub wF/sup 2// = 0.066. The four metal atoms form a tetrahedron with the apical Fe atom additionally bonded to three terminal carbonyl groups. Each Co atom is further bonded to one terminal and two bridging carbonyl ligands, as well as one phosphite group and the hydride ligand. The hydride ligand is located outside the metal cluster, 0.978 (3) A from the Co/sub 3/ face. This result confirms that of an earlier x-ray investigation by Huie, Knobler, and Kaesz. The Co--H distances are 1.724 (3), 1.731 (3), and 1.728 (3) A, and Co--H--Co angles are 92.1 (1), 91.7 (1), and 91.5 (1)/sup 0/.

A neutron diffraction study of HFeCo3(CO)9(P(OCH3)3)3, a metal cluster complex with a triply bridging hydride ligand

Tris(triisopropylsilyl)silane and the Generation of Bis(triisopropylsilyl)silylene

A neutron diffraction study of the 1 : 1 complex between 9‐methyladenine and 1‐methylthymine, C6H7N5· C6H8N2O2, has been carried out. The structure is monoclinic, space group P21/m, with two base pairs per unit cell; cell parameters a =8.304(2), b =6.552(2), c =12.837(3)A, and β=106.83(5)°. The structure has been refined by full‐matrix least squares techniques starting from the x‐ray results of Hoogsteen [K. Hoogsteen, Acta Crystallogr. 12, 822 (1959); Acta Crystallogr. 16, 907 (1963)]. All hydrogen atoms have been located with a precision better than 0.01 A, with the exception of methyl group hydrogens. The thymine molecules appear to be slightly disordered by means of a 180° rotation about N3 ··· C6, which has the effect of interchanging N1 and C5 while leaving the positions of all other atoms approximately unchanged. Between 10% and 13% of the thymine molecules in the structure are disordered in this way. Average refined neutron scattering lengths for nitrogen and carbon are bN=0.910(3) and bC=0.657(...

Precision neutron diffraction structure determination of protein and nucleic acid components. XII. A study of hydrogen bonding in the purine‐pyrimidine base pair 9‐methyladenine · 1‐methylthymine

Thomas F. Koetzle

Papers

Neutron diffraction analysis of (H/sub 3/Pt/sub 2/(Ph/sub 2/PCh/sub 2/CH/sub 2/PPh/sub 2/)/sub 2/)/sup +/(BPh/sub 4/): an unusual example of an unsymmetrical (P/sub 2/Pt(. mu. -H)/sub 2/PtP/sub 2/H) core

A neutron diffraction study of HFeCo3(CO)9(P(OCH3)3)3, a metal cluster complex with a triply bridging hydride ligand

Tris(triisopropylsilyl)silane and the Generation of Bis(triisopropylsilyl)silylene

Precision neutron diffraction structure determination of protein and nucleic acid components. XII. A study of hydrogen bonding in the purine‐pyrimidine base pair 9‐methyladenine · 1‐methylthymine

Deformation electron density of α-glycylglycine at 82 K. I. The neutron diffraction study