Journal ArticleDOI
MOLMOL: a program for display and analysis of macromolecular structures.
TLDR
Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, and identification and listing of short distances between pairs of hydrogen atoms.About:
This article is published in Journal of Molecular Graphics.The article was published on 1996-02-01. It has received 7111 citations till now. The article focuses on the topics: Molecular graphics.read more
Citations
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AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR
TL;DR: The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR, and their outputs include a detailed breakdown of the restraint violations.
Journal ArticleDOI
Intrinsically unstructured proteins and their functions.
H. Jane Dyson,Peter E. Wright +1 more
TL;DR: Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold, whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.
Journal ArticleDOI
Torsion angle dynamics for nmr structure calculation with the new program dyana
TL;DR: Test calculations starting from conformers with random torsion angle values showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures.
Journal ArticleDOI
Peptide Antimicrobial Agents
TL;DR: The structural requirements of peptides for antiviral and antibacterial activities are evaluated in light of the diverse set of primary and secondary structures described for host defense peptides.
Journal ArticleDOI
3D structure of Alzheimer's amyloid-β(1–42) fibrils
Thorsten Lührs,Christiane Ritter,Marc Adrian,Dominique Riek-Loher,Bernd Bohrmann,Heinz Döbeli,David Schubert,Roland Riek +7 more
TL;DR: The 3D structure of the fibrils comprising Aβ(1–42), which was obtained by using hydrogen-bonding constraints from quenched hydrogen/deuterium-exchange NMR, side-chain packing constraints from pairwise mutagenesis studies, and parallel, in-register β-sheet arrangement from previous solid-state NMR studies, explains the sequence selectivity, the cooperativity, and the apparent unidirectionality of Aβ fibril growth.
References
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Journal ArticleDOI
Optimization by Simulated Annealing
TL;DR: There is a deep and useful connection between statistical mechanics and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters), and a detailed analogy with annealing in solids provides a framework for optimization of very large and complex systems.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: 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 is developed.
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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
TL;DR: The MOLSCRIPT program as discussed by the authors produces plots of protein structures using several different kinds of representations, including simple wire models, ball-and-stick models, CPK models and text labels.
Proceedings ArticleDOI
Marching cubes: A high resolution 3D surface construction algorithm
TL;DR: In this paper, a divide-and-conquer approach is used to generate inter-slice connectivity, and then a case table is created to define triangle topology using linear interpolation.
Journal ArticleDOI
Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.