Induced peptide conformations in different antibody complexes: molecular modeling of the three-dimensional structure of peptide-antibody complexes using NMR-derived distance restraints.

PubWeight™: 0.97‹?› | Rank: Top 15%

🔗 View Article (PMID 1379072)

Published in Biochemistry on August 04, 1992

Authors

T Scherf1, R Hiller, F Naider, M Levitt, J Anglister

Author Affiliations

1: Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Articles by these authors

(truncated to the top 100)

The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res (2000) 11.38

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol (1976) 9.91

p53: a frequent target for genetic abnormalities in lung cancer. Science (1989) 7.51

A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol (1976) 7.06

Structure of nucleosome core particles of chromatin. Nature (1977) 6.24

Structural patterns in globular proteins. Nature (1976) 5.95

Studies on the mechanism of action of nalidixic acid. Antimicrob Agents Chemother (1973) 5.64

Dietary carotenoids, vitamins A, C, and E, and advanced age-related macular degeneration. Eye Disease Case-Control Study Group. JAMA (1994) 5.43

Computer simulation of protein folding. Nature (1975) 5.34

Conformations of immunoglobulin hypervariable regions. Nature (1990) 5.31

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature (1999) 5.03

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J Mol Biol (1985) 4.56

Helix to helix packing in proteins. J Mol Biol (1981) 4.24

Conformational preferences of amino acids in globular proteins. Biochemistry (1978) 4.00

Desire for death in the terminally ill. Am J Psychiatry (1995) 3.87

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

Detailed molecular model for transfer ribonucleic acid. Nature (1969) 3.81

Measuring the quality of life of cancer patients: the Functional Living Index-Cancer: development and validation. J Clin Oncol (1984) 3.76

How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc Natl Acad Sci U S A (1978) 3.55

Refinement of protein conformations using a macromolecular energy minimization procedure. J Mol Biol (1969) 3.21

The PRESAGE database for structural genomics. Nucleic Acids Res (1999) 3.03

The barriers in protein folding. Nat Struct Biol (1994) 2.79

Risk factors for hemiretinal vein occlusion: comparison with risk factors for central and branch retinal vein occlusion: the eye disease case-control study. Ophthalmology (1998) 2.62

Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci (1998) 2.60

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

Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Curr Biol (1993) 2.53

Protein folding by restrained energy minimization and molecular dynamics. J Mol Biol (1983) 2.51

Molecular dynamics of native protein. II. Analysis and nature of motion. J Mol Biol (1983) 2.29

Automatic identification of secondary structure in globular proteins. J Mol Biol (1977) 2.25

Energy refinement of hen egg-white lysozyme. J Mol Biol (1974) 2.24

Sunlight and cataract: an epidemiologic investigation. Am J Epidemiol (1977) 2.23

A humanized antibody that binds to the interleukin 2 receptor. Proc Natl Acad Sci U S A (1989) 2.23

Stabilization of phage T4 lysozyme by engineered disulfide bonds. Proc Natl Acad Sci U S A (1989) 2.17

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

The PTR family: a new group of peptide transporters. Mol Microbiol (1995) 2.02

Molecular dynamics simulation of photodissociation of carbon monoxide from hemoglobin. Proc Natl Acad Sci U S A (1985) 1.94

A brighter future for protein structure prediction. Nat Struct Biol (1999) 1.93

Molecular dynamics simulations of helix denaturation. J Mol Biol (1992) 1.92

The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J Mol Biol (1995) 1.92

Periodicity of deoxyribonuclease I digestion of chromatin. Science (1979) 1.90

Polyoxin D inhibits growth of zoopathogenic fungi. Antimicrob Agents Chemother (1983) 1.89

Molecular dynamics of native protein. I. Computer simulation of trajectories. J Mol Biol (1983) 1.87

Epidemiologic associations with nuclear, cortical, and posterior subcapsular cataracts. Am J Epidemiol (1986) 1.86

The complexity and accuracy of discrete state models of protein structure. J Mol Biol (1995) 1.86

Recognizing native folds by the arrangement of hydrophobic and polar residues. J Mol Biol (1995) 1.85

Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol (1997) 1.84

Computer simulation of DNA double-helix dynamics. Cold Spring Harb Symp Quant Biol (1983) 1.81

Climate change and the integrity of science. Science (2010) 1.80

A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci U S A (1992) 1.80

L-phenylalanine mustard (L-PAM) in the management of primary breast cancer. An update of earlier findings and a comparison with those utilizing L-PAM plus 5-fluorouracil (5-FU). Cancer (1977) 1.74

Significance of C-terminal cysteine modifications to the biological activity of the Saccharomyces cerevisiae a-factor mating pheromone. Mol Cell Biol (1991) 1.70

Senile lens changes and diabetes in two population studies. Am J Ophthalmol (1981) 1.69

Utilization of methionine-containing peptides and their derivatives by a methionine-requiring auxotroph of Saccharomyces cerevisiae. J Biol Chem (1974) 1.68

The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science (1986) 1.68

Protein unfolding pathways explored through molecular dynamics simulations. J Mol Biol (1993) 1.67

Expectations from structural genomics. Protein Sci (2000) 1.65

Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature (1991) 1.65

Clinical course of macular holes: the Eye Disease Case-Control Study. Arch Ophthalmol (1999) 1.64

Exploring conformational space with a simple lattice model for protein structure. J Mol Biol (1994) 1.63

Expression and purification of the Saccharomyces cerevisiae alpha-factor receptor (Ste2p), a 7-transmembrane-segment G protein-coupled receptor. J Biol Chem (1997) 1.56

A model of the molten globule state from molecular dynamics simulations. Proc Natl Acad Sci U S A (1992) 1.56

Solid-state NMR evidence for an antibody-dependent conformation of the V3 loop of HIV-1 gp120. Nat Struct Biol (1999) 1.56

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water. Proc Natl Acad Sci U S A (2001) 1.55

Proline-dependent structural and biological properties of peptides and proteins. Crit Rev Biochem Mol Biol (1993) 1.54

A new class of tyrosine hydroxylase inhibitors and a simple assay of inhibition in vivo. Biochem Pharmacol (1967) 1.54

De novo protein design. II. Plasticity in sequence space. J Mol Biol (1999) 1.53

Multiplicity of oligopeptide transport systems in Escherichia coli. J Bacteriol (1975) 1.51

Isolation and characterization of a Saccharomyces cerevisiae peptide transport gene. Mol Cell Biol (1994) 1.49

Fungal lipopeptide mating pheromones: a model system for the study of protein prenylation. Microbiol Rev (1995) 1.48

Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct (1993) 1.46

Systemic hypertension and age-related maculopathy in the Framingham Study. Arch Ophthalmol (1986) 1.45

A structural census of the current population of protein sequences. Proc Natl Acad Sci U S A (1997) 1.44

An Arabidopsis peptide transporter is a member of a new class of membrane transport proteins. Plant Cell (1994) 1.42

Epidemiologic associations with cataract in the 1971-1972 National Health and Nutrition Examination Survey. Am J Epidemiol (1983) 1.42

Discontinuation of antistreptococcal prophylaxis. A double-blind study in rheumatic patients free of heart disease. JAMA (1966) 1.42

Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. Proc Int Conf Intell Syst Mol Biol (1996) 1.41

Making up inotrope solutions. Anaesthesia (1992) 1.39

Molecular dynamics of hydrogen bonds in bovine pancreatic trypsin inhibitor protein. Nature (1981) 1.38

Pre-operative chemo-radiotherapy in locally advanced rectal cancer: is this the way of future management? Australas Radiol (1999) 1.38

Practice parameters for the management of colonic cancer I: surgical issues. Recommendations of the Colorectal Surgical Society of Australia. Aust N Z J Surg (1999) 1.38

Superiority of alternating non-cross-resistant chemotherapy in extensive small cell lung cancer. A multicenter, randomized clinical trial by the National Cancer Institute of Canada. Ann Intern Med (1987) 1.38

De novo protein design. I. In search of stability and specificity. J Mol Biol (1999) 1.37

Cloning of a second Arabidopsis peptide transport gene. Plant Physiol (1996) 1.36

Blindness caused by diabetic retinopathy. Am J Ophthalmol (1974) 1.36

Stereospecificity of tripeptide utilization in a methionine auxotroph of Escherichia coli K-12. J Bacteriol (1974) 1.35

Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng (1989) 1.34

Proline-rich peptide from the coral pathogen Vibrio shiloi that inhibits photosynthesis of Zooxanthellae. Appl Environ Microbiol (2001) 1.33

Effect of proline residues on protein folding. J Mol Biol (1981) 1.33

Blindness from glaucoma. Am J Ophthalmol (1975) 1.30

Integrating the equations of motion. J Mol Biol (1983) 1.29

Synthesis and biological activity of tripeptidyl polyoxins as antifungal agents. Antimicrob Agents Chemother (1983) 1.26

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J Mol Biol (1996) 1.26

Ab initio protein structure prediction using a combined hierarchical approach. Proteins (1999) 1.26

Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol (1999) 1.24

Pseudoexfoliation, intraocular pressure, and senile lens changes in a population-based survey. Arch Ophthalmol (1982) 1.24

Substrate recognition by oligosaccharyl transferase. Inhibition of co-translational glycosylation by acceptor peptides. J Biol Chem (1983) 1.23

An oligopeptide transport gene from Candida albicans. Microbiology (1997) 1.23

Reversible alkylation of a methionyl residue near the active site of -galactosidase. Biochemistry (1972) 1.23

Regulation of dipeptide transport in Saccharomyces cerevisiae by micromolar amino acid concentrations. J Bacteriol (1987) 1.21