Taxonomy and conformational analysis of loops in proteins.

Modeling of loops in protein structures. Protein Sci (2000) 9.68

Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics (2006) 8.72

Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci (2003) 4.82

Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci U S A (2002) 3.23

The structure of the acto-myosin subfragment 1 complex: results of searches using data from electron microscopy and x-ray crystallography. Proc Natl Acad Sci U S A (1997) 1.44

Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases. Nucleic Acids Res (2000) 1.35

Origins of structural diversity within sequentially identical hexapeptides. Protein Sci (1993) 1.18

Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core. J Biol Chem (2004) 1.10

Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. Protein Sci (2002) 0.99

Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics (2016) 0.95

Physical-chemical determinants of turn conformations in globular proteins. Protein Sci (2007) 0.91

Does conformational free energy distinguish loop conformations in proteins? Biophys J (1997) 0.89

Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade. PLoS One (2012) 0.86

Stabilization of a strained protein loop conformation through protein engineering. Protein Sci (1995) 0.86

Early-stage folding in proteins (in silico) sequence-to-structure relation. J Biomed Biotechnol (2005) 0.84

Conformational sampling in template-free protein loop structure modeling: an overview. Comput Struct Biotechnol J (2013) 0.83

Analysis of loop boundaries using different local structure assignment methods. Protein Sci (2009) 0.82

The radius of gyration of native and reductively methylated myosin subfragment-1 from neutron scattering. Biophys J (1995) 0.81

Linkers of secondary structures in proteins. Protein Sci (1997) 0.79

Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. J Phys Chem B (2006) 0.78

How long is a piece of loop? PeerJ (2013) 0.77

Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding. Biophysics (Nagoya-shi) (2006) 0.75

Proline-rich tandem repeats of antibody complementarity-determining regions bind and neutralize human immunodeficiency virus type 1 particles. J Virol (1996) 0.75

Identification and characterization of two novel bla(KLUC) resistance genes through large-scale resistance plasmids sequencing. PLoS One (2012) 0.75

MOLS sampling and its applications in structural biophysics. Biophys Rev (2010) 0.75

How many hydrogen-bonded α-turns are possible? J Mol Model (2010) 0.75

Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proc Natl Acad Sci U S A (1993) 10.36

An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol (1996) 9.31

Eight prion strains have PrP(Sc) molecules with different conformations. Nat Med (1998) 9.01

Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci (1997) 7.92

A geometric approach to macromolecule-ligand interactions. J Mol Biol (1982) 5.71

Prion propagation in mice expressing human and chimeric PrP transgenes implicates the interaction of cellular PrP with another protein. Cell (1995) 5.16

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol (1997) 4.79

Prion protein biology. Cell (1998) 4.20

Improvements in protein secondary structure prediction by an enhanced neural network. J Mol Biol (1990) 4.10

Structure of the recombinant full-length hamster prion protein PrP(29-231): the N terminus is highly flexible. Proc Natl Acad Sci U S A (1997) 4.10

Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation. Proc Natl Acad Sci U S A (1997) 3.78

Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform. Proc Natl Acad Sci U S A (1997) 3.42

Acridine and phenothiazine derivatives as pharmacotherapeutics for prion disease. Proc Natl Acad Sci U S A (2001) 3.39

Co-evolution of proteins with their interaction partners. J Mol Biol (2000) 3.23

A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform. J Mol Biol (1997) 2.95

Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel. J Mol Biol (1999) 2.92

Strain-specified relative conformational stability of the scrapie prion protein. Protein Sci (2001) 2.60

Copper binding to the prion protein: structural implications of four identical cooperative binding sites. Proc Natl Acad Sci U S A (1999) 2.44

Prion protein gene variation among primates. J Mol Biol (1995) 2.43

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res (2001) 2.37

Prion protein selectively binds copper(II) ions. Biochemistry (1998) 2.32

Recombinant scrapie-like prion protein of 106 amino acids is soluble. Proc Natl Acad Sci U S A (1996) 2.12

Physical and enzymatic studies on poly d(I-C)-poly d(I-C), an unusual double-helical DNA. Nature (1970) 2.04

Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (1987) 2.04

Identification of the Cu2+ binding sites in the N-terminal domain of the prion protein by EPR and CD spectroscopy. Biochemistry (2000) 2.02

Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science (1998) 2.01

Free energy calculations by computer simulation. Science (1987) 1.98

COOH-terminal sequence of the cellular prion protein directs subcellular trafficking and controls conversion into the scrapie isoform. Proc Natl Acad Sci U S A (1997) 1.89

High-level expression and characterization of a purified 142-residue polypeptide of the prion protein. Biochemistry (1996) 1.87

Prion protein of 106 residues creates an artifical transmission barrier for prion replication in transgenic mice. Cell (1999) 1.87

Identification of a prion protein epitope modulating transmission of bovine spongiform encephalopathy prions to transgenic mice. Proc Natl Acad Sci U S A (1997) 1.87

Solution structure of Syrian hamster prion protein rPrP(90-231). Biochemistry (1999) 1.86

Folding of prion protein to its native alpha-helical conformation is under kinetic control. J Biol Chem (2001) 1.84

Four helix bundle diversity in globular proteins. J Mol Biol (1994) 1.84

Heritable disorder resembling neuronal storage disease in mice expressing prion protein with deletion of an alpha-helix. Nat Med (1997) 1.83

Selective neuronal targeting in prion disease. Neuron (1997) 1.82

Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci U S A (1993) 1.82

Elimination of prions by branched polyamines and implications for therapeutics. Proc Natl Acad Sci U S A (1999) 1.73

Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example. J Mol Biol (1979) 1.72

Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proc Natl Acad Sci U S A (1998) 1.70

Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor. J Cell Biol (1993) 1.68

A synthetic peptide initiates Gerstmann-Sträussler-Scheinker (GSS) disease in transgenic mice. J Mol Biol (2000) 1.65

Turn prediction in proteins using a pattern-matching approach. Biochemistry (1986) 1.65

A combinatorial approach to the discovery of efficient cationic peptoid reagents for gene delivery. Proc Natl Acad Sci U S A (1998) 1.65

Prion protein peptides induce alpha-helix to beta-sheet conformational transitions. Biochemistry (1995) 1.64

Binding of neural cell adhesion molecules (N-CAMs) to the cellular prion protein. J Mol Biol (2001) 1.63

Identification of two prion protein regions that modify scrapie incubation time. J Virol (2001) 1.63

The structure of a DNA-RNA hybrid. Proc Natl Acad Sci U S A (1967) 1.61

Hydrogen bonds involving sulfur atoms in proteins. Proteins (1991) 1.58

Copper binding to octarepeat peptides of the prion protein monitored by mass spectrometry. Protein Sci (2000) 1.57

Conformational transitions in peptides containing two putative alpha-helices of the prion protein. J Mol Biol (1995) 1.57

In vitro antimalarial activity of chalcones and their derivatives. J Med Chem (1995) 1.56

Electrostatic potential molecular surfaces. Proc Natl Acad Sci U S A (1982) 1.53

Separation of scrapie prion infectivity from PrP amyloid polymers. J Mol Biol (1996) 1.52

The prion folding problem. Curr Opin Struct Biol (1997) 1.52

Dominant-negative inhibition of prion formation diminished by deletion mutagenesis of the prion protein. J Virol (2000) 1.52

Solid-state NMR studies of the secondary structure of a mutant prion protein fragment of 55 residues that induces neurodegeneration. Proc Natl Acad Sci U S A (2001) 1.51

Chalcone, acyl hydrazide, and related amides kill cultured Trypanosoma brucei brucei. Mol Med (2000) 1.49

Physical studies of conformational plasticity in a recombinant prion protein. Biochemistry (1997) 1.48

X-ray diffraction of scrapie prion rods and PrP peptides. J Mol Biol (1995) 1.47

Two different neurodegenerative diseases caused by proteins with similar structures. Proc Natl Acad Sci U S A (2001) 1.44

Mimicking dominant negative inhibition of prion replication through structure-based drug design. Proc Natl Acad Sci U S A (2000) 1.41

Conic: a fast renderer for space-filling molecules with shadows. J Mol Graph (1991) 1.40

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proc Natl Acad Sci U S A (1998) 1.40

A human gene (AHNAK) encoding an unusually large protein with a 1.2-microns polyionic rod structure. Proc Natl Acad Sci U S A (1992) 1.40

X-ray fiber diffraction evidence for neighbor exclusion binding of a platinum metallointercalation reagent to DNA. Proc Natl Acad Sci U S A (1975) 1.39

Protein model structure evaluation using the solvation free energy of folding. Proc Natl Acad Sci U S A (1990) 1.38

Thermodynamics of model prions and its implications for the problem of prion protein folding. J Mol Biol (1999) 1.38

Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance. Biochem J (1981) 1.38

Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. J Mol Biol (1990) 1.38

Doppel is an N-glycosylated, glycosylphosphatidylinositol-anchored protein. Expression in testis and ectopic production in the brains of Prnp(0/0) mice predisposed to Purkinje cell loss. J Biol Chem (2000) 1.38

A surface of minimum area metric for the structural comparison of proteins. J Mol Biol (1996) 1.38

Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry (2001) 1.37

Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996. Fold Des (1997) 1.36

Identification of functional surfaces of the zinc binding domains of intracellular receptors. J Mol Biol (1997) 1.36

Proposed three-dimensional structure for the cellular prion protein. Proc Natl Acad Sci U S A (1994) 1.35

Chiral N-substituted glycines can form stable helical conformations. Fold Des (1997) 1.34

Pairwise sequence alignment below the twilight zone. J Mol Biol (2001) 1.32

Branched polyamines cure prion-infected neuroblastoma cells. J Virol (2001) 1.32

Real-time color graphics in studies of molecular interactions. Science (1981) 1.31

X-ray diffraction studies of double helical ribonucleic acid. Nature (1966) 1.31

Novel method for the rapid evaluation of packing in protein structures. J Mol Biol (1990) 1.30

Topological distribution of four-alpha-helix bundles. Proc Natl Acad Sci U S A (1989) 1.29

Mapping the early steps in the pH-induced conformational conversion of the prion protein. Proc Natl Acad Sci U S A (2001) 1.28

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

Analysis and prediction of protein beta-sheet structures by a combinatorial approach. Nature (1980) 1.27

Prion protein (PrP) synthetic peptides induce cellular PrP to acquire properties of the scrapie isoform. Proc Natl Acad Sci U S A (1995) 1.25

Scrapie prions: a three-dimensional model of an infectious fragment. Fold Des (1996) 1.24

Protein folding. Effect of packing density on chain conformation. J Mol Biol (1991) 1.24

Identification of candidate proteins binding to prion protein. Neurobiol Dis (1997) 1.23

On the use of chemically derived distance constraints in the prediction of protein structure with myoglobin as an example. J Mol Biol (1980) 1.23

Erythropoietin structure-function relationships. Mutant proteins that test a model of tertiary structure. J Biol Chem (1993) 1.21

Analysis of protein dimerization and ligand binding of orphan receptor HNF4alpha. J Mol Biol (2000) 1.21

Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science (1983) 1.19

Origins of structural diversity within sequentially identical hexapeptides. Protein Sci (1993) 1.18

Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sci U S A (1996) 1.18

High-resolution autoreactive epitope mapping and structural modeling of the 65 kDa form of human glutamic acid decarboxylase. J Mol Biol (1999) 1.16

The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search. J Mol Biol (1994) 1.14