PISCES: a protein sequence culling server

Wang, Guoli; Dunbrack, Roland L.

doi:10.1093/bioinformatics/btg224

Cited by 1,599 publications

(1,356 citation statements)

References 15 publications

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“…All φ,ψ-angles were determined in a nonredundant set of high-resolution X-ray crystal structures (19), and those within the bridge region were compared with results from simulations (Fig. 3).…”

Section: Resultsmentioning

confidence: 99%

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Porter

Rose

2010

Proc. Natl. Acad. Sci. U.S.A.

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A protein backbone has two degrees of conformational freedom per residue, described by its φ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate ¾ of φ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of φ,ψ-space for a blocked peptide; for conformers within this region, an amide hydrogen is solvent-inaccessible, depriving it of a hydrogen-bonding partner. Yet, this "forbidden" region is well populated in folded proteins, which can provide longer-range intramolecular hydrogen-bond partners for these otherwise unsatisfied polar groups. Consequently, conformational space expands under folding conditions, a paradigm-shifting realization that prompts an experimentally verifiable conjecture about likely folding pathways.protein folding | hydrogen bonding | β-turns | helix nucleation

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Section: Resultsmentioning

confidence: 99%

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Porter

Rose

2010

Proc. Natl. Acad. Sci. U.S.A.

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“…A Ramachandran plot showing the distribution of glycine or alanine φ/ψ angles in protein crystal structures was constructed based on a subset of proteins from a PDB database, with high resolution (<1.6 Å), small R-factor (<0.25) and less than 20% sequence homology 40,41 . Dihedral plots based on this statistical survey of the PDB provide experimental indication of which values of backbone torsions are commonly found in proteins.…”

Section: Dihedral Plots and Free Energy Surfacesmentioning

confidence: 99%

Comparison of multiple Amber force fields and development of improved protein backbone parameters

et al. 2006

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The ff94 force field that is commonly associated with the AMBER simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over stabilization of α-helices, were reported by us and other researchers. This led to a number of attempts to improve these parameters, resulting in a variety of "AMBER" force fields and significant difficulty in determining which should be used for a particular application. We show that several of these continue to suffer from inadequate balance between different secondary structure elements. In addition, the approach used in most of these studies neglected to account for the existence in AMBER of two sets of backbone φ/ψ dihedral terms. This led to parameter sets that provide unreasonable conformational preferences for glycine. We report here an effort to improve the φ/ψ dihedral terms in the ff99 energy function. Dihedral term parameters are based on fitting the energies of multiple conformations of glycine and alanine tetrapeptides from high level ab-initio quantum mechanical calculations. The new parameters for backbone dihedrals replace those in the existing ff99 force field. This parameter set, which we denote ff99SB, achieves a better balance of secondary structure elements as judged by improved distribution of backbone dihedrals for glycine and alanine with respect to PDB survey data. It also accomplishes improved agreement with published experimental data for conformational preferences of short alanine peptides, and better accord with experimental NMR relaxation data of test protein systems.

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“…As it appears from Supplementary Table 5, 80% (of which 17.5% are at ends) of the bonds in 4 À a are involved in a-helixes, 39.5% (of which 35.5% are at ends) in 3 10 helixes. The majority of bonds from 5 À d and half of the bonds in 5 À e and B30% of the bonds from 5 À b are involved in p-helices.…”

Section: Article Nature Communications | Doi: 101038/ncomms6803mentioning

confidence: 91%

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

et al. 2014

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Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each C a effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

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PISCES: a protein sequence culling server

Cited by 1,599 publications

References 15 publications

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

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