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

Crystal structure of (hrh(p(o-1-c3h7)3)2)2. a neutron diffraction study

Transition metal σ complexes are ubiquitous intermediates in metal-catalyzed reactions, including hydrogenations, activation and functionalization reactions of hydrocarbons, and hydroborations. For over 20 years, single-crystal neutron diffraction has been exploited to investigate bond activation in these systems. Topics investigated include H–H activation in H 2 complexes, C–H activation in agostic systems and, most recently, B–H activation in a catecholborane metal complex. These results are illustrated here drawing upon studies carried out at both pulsed neutron sources and steady-state reactors. Despite notable successes such as those that we highlight, however, single-crystal neutron diffraction has seen somewhat limited application here to date primarily due to the need for large crystals. Revolutionary improvements are anticipated with the advent of a new generation of sources including the Spallation Neutron Source (SNS) that is scheduled to become operational at Oak Ridge, TN in 2006. At the SNS, it will be possible to work with crystals approaching the size commonly used in X-ray studies employing laboratory sources and to greatly expand the range of materials that are open to investigation.

Single-crystal neutron diffraction: a valuable tool for probing bond activation in transition metal σ complexes

The role of transition metal atoms as hydrogen bond acceptors: A neutron diffraction study of [

Manual filing systems have drawbacks that make them inefficient. Take as an example a simple card file index of customer information. This depends on consistent use to be effective. For example, if the card always has the surname in the top left-hand corner then they are easy to put in alphabetical order. However, if some cards have the postcode in this position instead, the task becomes more complicated.

/pdf/benefits-of-databases-4q7nfbmah7.pdf

Benefits of databases

The structure of a La CuO single crystal with the excess oxygen content ys 0.03 has been studied by means of 24 qy neutron diffraction at Ts 13 K. Although the extra oxygen content of ys 0.03 is inside the miscibility gap of La CuO 24 qy

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Thomas F. Koetzle

Papers

Crystal structure of (hrh(p(o-1-c3h7)3)2)2. a neutron diffraction study

Single-crystal neutron diffraction: a valuable tool for probing bond activation in transition metal σ complexes

The role of transition metal atoms as hydrogen bond acceptors: A neutron diffraction study of [

Benefits of databases

Single‐Crystal Neutron Diffraction