Modeling antibody hypervariable loops: a combined algorithm.

PubWeight™: 1.50‹?› | Rank: Top 4%

🔗 View Article (PMC 298475)

Published in Proc Natl Acad Sci U S A on December 01, 1989

Authors

A C Martin1, J C Cheetham, A R Rees

Author Affiliations

1: Laboratory of Molecular Biophysics, University of Oxford, United Kingdom.

Articles citing this

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

A new clustering of antibody CDR loop conformations. J Mol Biol (2010) 1.83

CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci (2001) 1.53

Computer-aided antibody design. Protein Eng Des Sel (2012) 1.44

Modeling of protein loops by simulated annealing. Protein Sci (1993) 1.20

A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res (2006) 1.18

Humanization of murine monoclonal antibodies through variable domain resurfacing. Proc Natl Acad Sci U S A (1994) 1.17

Structural basis for autoantibody recognition of phosphatidylserine-beta 2 glycoprotein I and apoptotic cells. Proc Natl Acad Sci U S A (2001) 1.15

Modeling protein loops using a phi i + 1, psi i dimer database. Protein Sci (1995) 1.09

Peptide mimicry of the meningococcal group C capsular polysaccharide. Proc Natl Acad Sci U S A (1995) 1.03

Capsid antibodies to different adeno-associated virus serotypes bind common regions. J Virol (2013) 1.01

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A (1992) 0.99

A self-organizing algorithm for modeling protein loops. PLoS Comput Biol (2009) 0.96

Structural models of ribonuclease H domains in reverse transcriptases from retroviruses. Nucleic Acids Res (1991) 0.96

Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff. J Comput Chem (2013) 0.92

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

Crystal structure reveals conservation of amyloid-β conformation recognized by 3D6 following humanization to bapineuzumab. Alzheimers Res Ther (2014) 0.84

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

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity. PLoS Comput Biol (2011) 0.82

Improving predicted protein loop structure ranking using a Pareto-optimality consensus method. BMC Struct Biol (2010) 0.81

Molecular recognition of Candida albicans (1->2)-β-mannan oligosaccharides by a protective monoclonal antibody reveals the immunodominance of internal saccharide residues. J Biol Chem (2012) 0.81

Modeling of human anti-GBM antibody-alpha3(IV)NC1 interactions predicts antigenic cross-linking through contact of both heavy chains with repeating epitopes on alpha3(IV)NC1. Am J Nephrol (2009) 0.81

A modular perspective of protein structures: application to fragment based loop modeling. Methods Mol Biol (2013) 0.81

Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. Biochem J (2003) 0.79

Sampling multiple scoring functions can improve protein loop structure prediction accuracy. J Chem Inf Model (2011) 0.78

Genetic engineering of high affinity anti-human colorectal tumour mouse/human chimeric antibody. Immunology (1992) 0.76

Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities. J Comput Aided Mol Des (2000) 0.76

Clonal diversification in OspA-specific antibodies from peripheral circulation of a chronic Lyme arthritis patient. J Immunol Methods (2007) 0.76

Improving the binding affinity of an antibody using molecular modeling and site-directed mutagenesis. Protein Sci (1998) 0.76

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics (2017) 0.75

Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics (2017) 0.75

Structural predictions of the binding site architecture for monoclonal antibody NC6.8 using computer-aided molecular modeling, ligand binding, and spectroscopy. Biophys J (1995) 0.75

Structural models of antibody variable fragments: a method for investigating binding mechanisms. J Comput Aided Mol Des (1998) 0.75

Articles cited by this

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

The interpretation of protein structures: estimation of static accessibility. J Mol Biol (1971) 40.24

An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med (1970) 9.83

Using known substructures in protein model building and crystallography. EMBO J (1986) 7.36

Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol (1987) 6.42

Reshaping human antibodies for therapy. Nature (1988) 4.82

Three-dimensional structure of an antibody-antigen complex. Proc Natl Acad Sci U S A (1987) 3.48

Picosecond dynamics of tyrosine side chains in proteins. Biochemistry (1979) 3.35

Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers (1987) 2.53

Criteria that discriminate between native proteins and incorrectly folded models. Proteins (1988) 2.40

An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins (1986) 2.38

The galactan-binding immunoglobulin Fab J539: an X-ray diffraction study at 2.6-A resolution. Proteins (1986) 1.96

Hinge-bending in L-arabinose-binding protein. The "Venus's-flytrap" model. J Biol Chem (1982) 1.80

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

Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins (1986) 1.67

Structure of antibody hypervariable loops reproduced by a conformational search algorithm. Nature (1988) 1.61

Generation of an antibody with enhanced affinity and specificity for its antigen by protein engineering. Nature (1987) 1.07

Principles of antibody catalysis. Bioessays (1988) 1.05

The conformation of Salmonella O-antigenic polysaccharide chains of serogroups A, B, and D1 predicted by semi-empirical, Hard-Sphere (HSEA) calculations. Carbohydr Res (1984) 1.01

Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope. EMBO J (1986) 0.99

A three-dimensional model of an anti-lysozyme antibody. J Mol Biol (1987) 0.97

Nucleotide sequences of five anti-lysozyme monoclonal antibodies. EMBO J (1985) 0.93

Unusual joining sites in the H and L chains of an anti-lysozyme antibody. J Immunol (1988) 0.92

A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. Secondary structure motion in a 150 picosecond trajectory. J Mol Biol (1985) 0.91

Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme. Biochemistry (1988) 0.89

A refined model for the variable domains (Fv) of the J539 beta(1,6)-D-galactan-binding immunoglobulin. Mol Immunol (1984) 0.87

Articles by these authors

Efficiency of signalling through cytokine receptors depends critically on receptor orientation. Nature (1998) 2.65

Isolation and characterization of an Fc receptor from neonatal rat small intestine. Eur J Immunol (1985) 2.20

A new family of mouse homeo box-containing genes: molecular structure, chromosomal location, and developmental expression of Hox-7.1. Genes Dev (1989) 1.93

WAM: an improved algorithm for modelling antibodies on the WEB. Protein Eng (2000) 1.67

Epidermal growth factor receptors. Mol Cell Biochem (1981) 1.50

High affinity epidermal growth factor receptors on the surface of A431 cells have restricted lateral diffusion. EMBO J (1984) 1.46

Studies on the immunoglobulin-G Fc-fragment receptor from neonatal rat small intestine. Biochem J (1980) 1.35

Properties of a monoclonal antibody to epidermal growth factor receptor with implications for the mechanism of action of EGF. EMBO J (1984) 1.34

The hunchback and its neighbours: proline as an environmental modulator. Trends Biochem Sci (2001) 1.28

Epidermal growth factor receptors increase during the differentiation of embryonal carcinoma cells. Nature (1979) 1.27

V region sequences of anti-DNA and anti-RNA autoantibodies from NZB/NZW F1 mice. J Immunol (1988) 1.26

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations. J Mol Biol (1986) 1.25

The preparation of protected fragments of lysozyme for semisynthesis. Biochem J (1976) 1.18

Humanization of murine monoclonal antibodies through variable domain resurfacing. Proc Natl Acad Sci U S A (1994) 1.17

Short elastin-like peptides exhibit the same temperature-induced structural transitions as elastin polymers: implications for protein engineering. J Mol Biol (1998) 1.17

Subcellular distribution of the external and internal domains of the EGF receptor in A-431 cells. Exp Cell Res (1986) 1.15

The prediction and characterization of metal binding sites in proteins. Protein Eng (1993) 1.12

Generation of an antibody with enhanced affinity and specificity for its antigen by protein engineering. Nature (1987) 1.07

Reduced antibody response to streptavidin through site-directed mutagenesis. Protein Sci (2001) 1.05

Site-directed mutagenesis of proteolytic antibody light chain. J Mol Biol (1995) 1.03

Trifluoroethanol may form a solvent matrix for assisted hydrophobic interactions between peptide side chains. Protein Eng (2000) 1.03

Modelling of the combining sites of three anti-lysozyme monoclonal antibodies and of the complex between one of the antibodies and its epitope. EMBO J (1986) 0.99

Mapping T cell recognition: the identification of a T cell receptor residue critical to the specific interaction with an influenza hemagglutinin peptide. Eur J Immunol (1995) 0.96

A behavioural and biochemical study in rats of 5-hydroxytryptamine receptor agonists and antagonists, with observations on structure-activity requirements for the agonists. Br J Pharmacol (1981) 0.95

Appearance of functional insulin receptors during the differentiation of embryonal carcinoma cells. J Cell Biol (1981) 0.94

The semisynthesis of portions of hen's-egg lysozyme by fragment condensation. Biochem J (1976) 0.94

Nucleotide sequences of five anti-lysozyme monoclonal antibodies. EMBO J (1985) 0.93

Blood group-active carbohydrate chains on the receptor for epidermal growth factor of A431 cells. EMBO J (1984) 0.92

Monoclonal antibody (EGR/G49) reactive with the epidermal growth factor receptor of A431 cells recognizes the blood group ALeb and ALey structures. Mol Immunol (1985) 0.90

The role of the arginine-B22 residue in insulin action. Biochem J (1981) 0.90

Comparison of surface accessible residues in human and murine immunoglobulin Fv domains. Implication for humanization of murine antibodies. J Mol Biol (1994) 0.89

Molecular modeling of antibody combining sites. Methods Enzymol (1991) 0.89

Mechanistic studies of a tyrosine-dependent catalytic antibody. Biochemistry (1991) 0.88

Guided selection of a pan carcinoma specific antibody reveals similar binding characteristics yet structural divergence between the original murine antibody and its human equivalent. J Mol Biol (2000) 0.86

Vector-mediated drug delivery to the brain. Expert Opin Biol Ther (2001) 0.85

1H nuclear magnetic resonance studies of hen lysozyme-N-acetylglucosamine oligosaccharide complexes in solution. Application of chemical shifts for the comparison of conformational changes in solution and in the crystal. J Mol Biol (1994) 0.85

A comparison of two murine monoclonal antibodies humanized by CDR-grafting and variable domain resurfacing. Protein Eng (1996) 0.85

Three distinct epitopes within the loop region of hen egg lysozyme defined with monoclonal antibodies. EMBO J (1985) 0.85

X-ray crystallography and the amino acid sequence of lysozyme. Biochem J (1972) 0.84

Diazoalkanes in peptide semisynthesis. Biochem J (1976) 0.84

Recombinant antibodies as carrier proteins for sub-unit vaccines: influence of mode of fusion on protein production and T-cell activation. J Immunol Methods (2000) 0.83

Molecular modeling and preclinical evaluation of the humanized NR-LU-13 antibody. Clin Cancer Res (1999) 0.83

Factor VIII related antigen (von Willebrand's factor) in Kawasaki disease. Clin Pediatr (Phila) (1990) 0.82

Studies on the protease and other enzymes from the venom of Lethocerus cordofanus. Nature (1969) 0.82

Studies on the structure and function of the epidermal-growth-factor receptor. Biochem Soc Trans (1984) 0.81

Growth factors in mammalian embryogenesis. Ciba Found Symp (1985) 0.80

An engineered minidomain containing an elastin turn exhibits a reversible temperature-induced IgG binding. Biochemistry (1999) 0.79

Antigen mobility in the combining site of an anti-peptide antibody. Proc Natl Acad Sci U S A (1991) 0.79

Expression of mouse immunoglobulin light and heavy chain variable regions in Escherichia coli and reconstitution of antigen-binding activity. Protein Eng (1990) 0.78

Sodium sulphate reactivates a protein A minidomain with a short elastin beta-turn. Biochem Biophys Res Commun (2000) 0.78

Physicochemical characterization of the cytoplasmic domain of the epidermal growth factor receptor and evidence for conformational changes associated with its activation by ammonium sulphate. Biochem J (1995) 0.78

The relationship of erythrocyte insulin receptors to red cell age and to monocyte insulin receptors. Clin Endocrinol (Oxf) (1981) 0.78

Bradykinin blocks the action of EGF, but not PDGF, on fibroblast division. FEBS Lett (1989) 0.78

Proliferation of a human embryonal carcinoma-derived cell line in serum-free medium: inter-relationship between growth factor requirements and membrane receptor expression. J Cell Sci (1985) 0.77

Inhibition of activating transcription factor 1- and cAMP-responsive element-binding protein-activated transcription by an intracellular single chain Fv fragment. J Biol Chem (1998) 0.76

Properties of immunoglobulin G-Fc receptors from neonatal rat intestinal brush borders. Ciba Found Symp (1983) 0.76

The cloning and expression of an anti-peptide antibody: a system for rapid analysis of the binding properties of engineered antibodies. Protein Eng (1989) 0.76

Engineering a soluble extracellular erythropoietin receptor (EPObp) in Pichia pastoris to eliminate microheterogeneity, and its complex with erythropoietin. Protein Eng (1999) 0.76

Use of two-dimensional 1H nuclear magnetic resonance to study high-affinity antibody-peptide interactions. Methods Enzymol (1991) 0.76

Engineering antibody affinity and specificity. Int J Cancer Suppl (1988) 0.75

Molecular modeling of antibody-combining sites. Methods Mol Biol (1995) 0.75

Antibody-combining sites: prediction and design. Biochem Soc Symp (1990) 0.75

Potentiometric biosensor employing catalytic antibodies as the molecular recognition element. Anal Chem (1990) 0.75

Second structure determinations. Protein Eng (1989) 0.75

Antibody-combining sites. Extending the natural limits. Appl Biochem Biotechnol (1994) 0.75

Transmission error in the photometric estimation of leaf area. Plant Physiol (1966) 0.75

Crystallization of the Fab fragments of anti-peptide monoclonal antibodies and a complex with peptide. J Mol Biol (1992) 0.75

Characterization of the mechanism of action of a catalytic antibody. Ciba Found Symp (1991) 0.75