Helix-sheet packing in proteins.

Mining tertiary structural motifs for assessment of designability. Methods Enzymol (2013) 0.87

An amino acid packing code for α-helical structure and protein design. J Mol Biol (2012) 0.86

Rapid search for tertiary fragments reveals protein sequence-structure relationships. Protein Sci (2014) 0.84

Description of local and global shape properties of protein helices. J Mol Model (2013) 0.80

PackHelix: a tool for helix-sheet packing during protein structure prediction. Proteins (2011) 0.76

Tertiary alphabet for the observable protein structural universe. Proc Natl Acad Sci U S A (2016) 0.75

An amino acid code for irregular and mixed protein packing. Proteins (2015) 0.75

The Protein Data Bank. Nucleic Acids Res (2000) 187.10

The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol (1977) 90.57

SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88

CATH--a hierarchic classification of protein domain structures. Structure (1997) 29.95

Prediction of protein conformation. Biochemistry (1974) 20.51

Knowledge-based protein secondary structure assignment. Proteins (1995) 14.08

The structure of synthetic polypeptides. Proc Natl Acad Sci U S A (1951) 13.24

Atomic coordinates and structure factors for two helical configurations of polypeptide chains. Proc Natl Acad Sci U S A (1951) 8.98

Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98

Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature (1965) 8.13

A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature (1958) 5.64

The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci U S A (1951) 5.60

A database of protein structure families with common folding motifs. Protein Sci (1992) 4.77

Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution. Nature (1960) 4.20

Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol (1996) 3.86

Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins (1999) 3.79

A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol (2005) 3.69

The structure of hair, muscle, and related proteins. Proc Natl Acad Sci U S A (1951) 2.73

Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol (1996) 2.70

Structure of proteins: packing of alpha-helices and pleated sheets. Proc Natl Acad Sci U S A (1977) 2.60

The structure of feather rachis keratin. Proc Natl Acad Sci U S A (1951) 2.46

The structure of fibrous proteins of the collagen-gelatin group. Proc Natl Acad Sci U S A (1951) 2.25

Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci (2000) 2.10

Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol (2000) 2.05

Handedness of crossover connections in beta sheets. Proc Natl Acad Sci U S A (1976) 1.84

The polypeptide-chain configuration in hemoglobin and other globular proteins. Proc Natl Acad Sci U S A (1951) 1.68

A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol (2003) 1.46

A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol (2002) 1.37

A 'periodic table' for protein structures. Nature (2002) 1.36

On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit. J Mol Biol (1976) 1.34

Analysis and prediction of the packing of alpha-helices against a beta-sheet in the tertiary structure of globular proteins. J Mol Biol (1982) 1.28

An atomic environment potential for use in protein structure prediction. J Mol Biol (2005) 1.19

Prediction of protein structure from ideal forms. Proteins (2008) 1.16

Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun (2006) 1.16

Packing of secondary structural elements in proteins. Analysis and prediction of inter-helix distances. J Mol Biol (1993) 1.10

Influence of protein structure databases on the predictive power of statistical pair potentials. Proteins (1998) 1.08

Distributions of beta sheets in proteins with application to structure prediction. Proteins (2002) 1.08

The dependence of all-atom statistical potentials on structural training database. Biophys J (2004) 1.06

Interactions between an alpha-helix and a beta-sheet. Energetics of alpha/beta packing in proteins. J Mol Biol (1985) 1.03

Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins (2004) 0.98

Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins. Protein Sci (1999) 0.92

Structural classification of alphabetabeta and betabetaalpha supersecondary structure units in proteins. Proteins (1998) 0.91

Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets. Protein Sci (2003) 0.86

ProteinShop: a tool for interactive protein manipulation and steering. J Comput Aided Mol Des (2004) 0.83

Global secondary structure packing angle bias in proteins. Proteins (2003) 0.79

The ASTRAL Compendium in 2004. Nucleic Acids Res (2004) 10.03

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins (2005) 6.57

ASTRAL compendium enhancements. Nucleic Acids Res (2002) 4.43

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J Mol Biol (2005) 4.02

Plant NBS-LRR proteins: adaptable guards. Genome Biol (2006) 3.38

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res (2006) 2.21

Small libraries of protein fragments model native protein structures accurately. J Mol Biol (2002) 1.87

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res (2006) 1.45

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J (2013) 1.37

Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics. Biophys J (2008) 1.36

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res (2007) 1.32

Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. BMC Mol Biol (2007) 1.24

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models. Nucleic Acids Res (2011) 1.20

The weighted-volume derivative of a space-filling diagram. Proc Natl Acad Sci U S A (2003) 1.11

Multi-scale clustering by building a robust and self correcting ultrametric topology on data points. PLoS One (2013) 1.01

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res (2005) 0.97

Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc Natl Acad Sci U S A (2009) 0.92

Structural alphabets for protein structure classification: a comparison study. J Mol Biol (2008) 0.90

A new lectin family with structure similarity to actinoporins revealed by the crystal structure of Xerocomus chrysenteron lectin XCL. J Mol Biol (2004) 0.88

Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif. J Biol Chem (2014) 0.85

Computational assembly of polymorphic amyloid fibrils reveals stable aggregates. Biophys J (2013) 0.85

Selective and specific ion binding on proteins at physiologically-relevant concentrations. FEBS Lett (2011) 0.85

Relaxed specificity in aromatic prenyltransferases. Nat Chem Biol (2005) 0.83

Globally optimal cortical surface matching with exact landmark correspondence. Inf Process Med Imaging (2013) 0.81

Computing ion solvation free energies using the dipolar Poisson model. J Phys Chem B (2009) 0.81

A quality metric for homology modeling: the H-factor. BMC Bioinformatics (2011) 0.80

Surface-histogram: a new shape descriptor for protein-protein docking. Proteins (2011) 0.78

Geometric measures of large biomolecules: surface, volume, and pockets. J Comput Chem (2011) 0.77

Sampling the conformation of protein surface residues for flexible protein docking. BMC Bioinformatics (2010) 0.77

Identifying essential pairwise interactions in elastic network model using the alpha shape theory. J Comput Chem (2014) 0.77

Protein side-chain modeling with a protein-dependent optimized rotamer library. Proteins (2014) 0.77

Morphing methods to visualize coarse-grained protein dynamics. Methods Mol Biol (2014) 0.76

An analytical method for computing atomic contact areas in biomolecules. J Comput Chem (2012) 0.76

The H-factor as a novel quality metric for homology modeling. J Clin Bioinforma (2012) 0.76

Extracting knowledge from protein structure geometry. Proteins (2013) 0.76

PackHelix: a tool for helix-sheet packing during protein structure prediction. Proteins (2011) 0.76

Capturing protein sequence-structure specificity using computational sequence design. Proteins (2013) 0.76

Adaptive Skin Meshes Coarsening for Biomolecular Simulation. Comput Aided Geom Des (2011) 0.75

His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics. Arch Biochem Biophys (2013) 0.75