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

Picosecond transient Raman spectra of photoexcited 4-dimethylamino-4′-nitrostilbene in polar solvents (acetonitrile, acetone and benzonitrile) were observed and the decay kinetics of the observed Raman bands were analysed. The observed solvent dependences of the peak positions suggest that the transient Raman bands arise from a non-radiative charge-transfer (CT) state. Molecules in the vibrationally excited CT states were also observed by monitoring transient anti-Stokes Raman scattering. These results indicate that a rapid non-radiative transition occurs from the lowest allowed singlet state to vibrationally excited CT states.

Picosecond transient Raman spectra of photoexcited 4‐dimethylamino‐4′‐nitrostilbene in polar solvents

Vibrational analysis is carried out for the radical anions of naphthalene-h8 and -d8. Their infrared (IR) spectra are observed in tetrahydrofuran by using a cell designed for IR measurements of unstable species. The vibrational force field and the IR intensities are calculated by the ab initio molecular orbital and density functional methods at various theoretical levels. As found in the cases of the radical cations of many polycyclic aromatic hydrocarbons (PAHs), a few strong IR bands with intensities of the order of 102 km mol1 are observed in the 1700900 cm1 region. These observed spectral features are well reproduced by the calculations at the CASSCF (complete active space self-consistent field) and B3LYP (Becke's three-parameter hybrid method using the LeeYangParr correlation functional) levels. The calculation at the B3LYP level gives a better fit between the observed and calculated absolute IR intensities. Normal modes and the origin of the strong IR intensities characteristic of the radical a...

Vibrational spectra and electronvibration interactions of the naphthalene radical anion Experimental and theoretical study

The Pr(III)- and Eu(III)-induced shifts of 1H nuclear magnetic resonances of thymidine 3′,5′-cyclic phosphate were observed in D2O solution. The results indicated that the induced shifts were primarily of dipolar origin and that the magnetic susceptibility tensor had effective axial symmetry. The ratios of shifts intrinsic to the lanthanide-substrate 1 : 1 complex were determined after correcting for the contributions of the complex formation shifts (diamagnetic terms). The Gd(III)-induced perturbations of the spin-lattice relaxation times were also observed, and the ratios of relaxation rates were obtained. A computer search was then performed to find out the molecular conformation of this cyclic nucleotide which best fitted the shift and relaxation ratios. As a result the phosphate-ring part was found to have a typical chair conformation. The effective symmetry axis of the magnetic susceptibility tensor coincided with the bisector of the OPO angle almost completely. It was rather difficult, however, to ...

Conformation of Thymidine 3′,5′-Cyclic Phosphate in Aqueous Solution. Compatibility of the Information from the Lanthanide-Ion Probe and the Spin-Coupling Constants

Mitsuo Tasumi

Papers

Picosecond transient Raman spectra of photoexcited 4‐dimethylamino‐4′‐nitrostilbene in polar solvents

Vibrational spectra and electronvibration interactions of the naphthalene radical anion Experimental and theoretical study

Conformation of Thymidine 3′,5′-Cyclic Phosphate in Aqueous Solution. Compatibility of the Information from the Lanthanide-Ion Probe and the Spin-Coupling Constants

Incoherent inelastic neutron scattering from polyacetylenes in the 3500- 400 cm−1 region

Infrared spectrum of cyclopropylamine