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

COMPLEX CHEMISTRY OF REACTIVE ORGANIC COMPOUNDS. 48. Σ-ALKYL, Π-ALLYL, AND Π-OLEFIN COORDINATION OF DIPHENYLKETENE: NEUTRON DIFFRACTION STUDIES OF THE CARBONYLIRON COMPLEXES FE(CO)3(η3:η1-(C6H5)2CCO) AND FE2(CO)6(CH(C6H5)(C6H4))

The crystal and molecular structure of the hexahydridoosmium complex (OsH/sub 6/(PC/sub 12/H/sub 19/)/sub 2/), determined from a low-temperature X-ray diffraction analysis, has been refined on the basis of neutron diffraction data obtained at 20 K. The dodecahedral ML/sub 2/H/sub 6/ core has approximate mm symmetry with the phosphines in equivalent B (five-neighbor) sites and a P-Os-P angle of 155.2 (1)/sup 0/. The Os-H distances range from 1.637 (4) to 1.668 (4) A, with a mean value of 1.649 (5) A. Crystal data at 20.0 (5) K: a = 17.016 (3) A, b = 13.762 (3) A, c = 10.857 (3) A, ..beta.. = 98.91 (2)/sup 0/, V = 2512 (1) A/sup 3/, monoclinic, P2/sub 1//n, Z = 4, M/sub r/ 584.8. 29 references, 2 figures, 3 tables.

Crystal and Molecular Structure of Bis(diisopropylphenylphosphine)hexahydridoosmium, (OsH6(PC12H19)2): Single-Crystal Neutron Diffraction Study at 20 K

Precision neutron diffraction structure determination of protein and nucleic acid components part 12, a study of hydrogen bonding in the purine-pyrimidine base pair 9-methyladenine, 1-methylthymine

The molecular and crystal structure of squaric acid (3,4‐dihydroxy‐3‐cyclobutene‐1,2‐dione) has been determined by neutron diffraction techniques at 121°C, a temperature above that of the monoclinic to tetragonal phase transition (∼100°C). The high‐temperature structure is in space group I4/m, a=c=6.137(2) A, b=5.337(2) A. Least‐squares refinement has been carried out with 25 variable parameters and 276 reflections, to yield an unweighted R value (on F2) of 0.042. The squaric acid molecule has point symmetry 4/m, and the hydrogen atom is ’’disordered’’ about the inversion center at the midpoint of the O⋅⋅⋅O hydrogen bond. Hydrogen‐bonding parameters are O–H 1.014(4), H⋅⋅⋅O 1.536(5) A, O⋅⋅⋅O 2.548(2) A, & O–H⋅⋅⋅O 176.2(6) °. The tetragonal structure corresponds closely to that obtained from the atomic parameters determined in the monoclinic phase at 25°C, by averaging over the pseudofourfold symmetry.

The molecular and crystal structure of squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione) at 121°c- a neutron diffraction study

The crystal and molecular structure of the pentahydrido complex ReH/sub 5/(PMePh/sub 2/)/sub 3/, has been determined by x-ray diffraction techniques at room temperature and refined against neutron diffraction data obtained at 20 K to yield precise locations for all atoms. The two independent molecules in the unit cell possess essentially identical dodecahedral cores, with the three phosphines and one hydride in B (5-neighbor) positions and the remaining four hydrides in A (4-neighbor) sites. The mean Re-H bond distance is 1.688 (5)A, which is in agreement with that found in K/sub 2/ReH/sub 9/(1.68(1)A). At convergence with anisotropic thermal parameters refined for all 174 atoms (1568 variables), agreement factors are presented for 11,374 independent neutron observations. Crystal data at 20.0(5)K are presented for the complex. In solution, /sup 1/H and /sup 31/P (/sup 1/H) NMR meausrements indicated that the compounds are fluxional molecules, with magnetically equivalent hydrides and phosphides at 25/sup 0/C.

Thomas F. Koetzle

Papers

COMPLEX CHEMISTRY OF REACTIVE ORGANIC COMPOUNDS. 48. Σ-ALKYL, Π-ALLYL, AND Π-OLEFIN COORDINATION OF DIPHENYLKETENE: NEUTRON DIFFRACTION STUDIES OF THE CARBONYLIRON COMPLEXES FE(CO)3(η3:η1-(C6H5)2CCO) AND FE2(CO)6(CH(C6H5)(C6H4))

Crystal and Molecular Structure of Bis(diisopropylphenylphosphine)hexahydridoosmium, (OsH6(PC12H19)2): Single-Crystal Neutron Diffraction Study at 20 K

Precision neutron diffraction structure determination of protein and nucleic acid components part 12, a study of hydrogen bonding in the purine-pyrimidine base pair 9-methyladenine, 1-methylthymine

The molecular and crystal structure of squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione) at 121°c- a neutron diffraction study

Pentahydridorhenium: crystal and molecular structure of reh5(pmeph2)3