Published in PLoS One on April 26, 2011
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A (1991) 119.63
Features and development of Coot. Acta Crystallogr D Biol Crystallogr (2010) 89.46
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics (2005) 34.83
CHARMM: the biomolecular simulation program. J Comput Chem (2009) 27.71
Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D Biol Crystallogr (2001) 21.01
Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr (2006) 16.41
The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science (1998) 12.52
Genome organization and transactivation of the human immunodeficiency virus type 2. Nature (1987) 11.79
HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc (2003) 11.65
Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell (1986) 10.70
CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5. Nature (1996) 10.27
Structure of an unliganded simian immunodeficiency virus gp120 core. Nature (2005) 8.30
Molecular architecture of native HIV-1 gp120 trimers. Nature (2008) 8.04
Isolation of a new human retrovirus from West African patients with AIDS. Science (1986) 7.97
Structure of a V3-containing HIV-1 gp120 core. Science (2005) 7.69
Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature (2006) 6.78
Principal neutralizing domain of the human immunodeficiency virus type 1 envelope protein. Proc Natl Acad Sci U S A (1989) 6.58
Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol (1987) 6.42
HTLV-III/LAV-neutralizing antibodies to an E. coli-produced fragment of the virus envelope. Science (1986) 6.33
Characterization of a human immunodeficiency virus neutralizing monoclonal antibody and mapping of the neutralizing epitope. J Virol (1988) 5.96
GP120: target for neutralizing HIV-1 antibodies. Annu Rev Immunol (2006) 5.28
HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins (2007) 3.97
Oligomeric modeling and electrostatic analysis of the gp120 envelope glycoprotein of human immunodeficiency virus. J Virol (2000) 3.52
Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A (1992) 3.42
Standard conformations for the canonical structures of immunoglobulins. J Mol Biol (1997) 3.42
Crystal structure of PG16 and chimeric dissection with somatically related PG9: structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1. J Virol (2010) 3.40
HIV vaccines. Annu Rev Immunol (2006) 3.31
Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D. Structure (2004) 3.31
V3: HIV's switch-hitter. AIDS Res Hum Retroviruses (2005) 3.00
Molecular dynamics of native protein. II. Analysis and nature of motion. J Mol Biol (1983) 2.29
Length distribution of CDRH3 in antibodies. Proteins (1993) 2.12
C-H...pi-interactions in proteins. J Mol Biol (2001) 2.06
Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable loops and the nature of the antigen. J Mol Biol (2003) 2.00
Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci (2008) 2.00
Major antigen-induced domain rearrangements in an antibody. Structure (1993) 1.99
Antibody elbow angles are influenced by their light chain class. J Mol Biol (2006) 1.96
Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. Mol Immunol (2008) 1.82
Conserved structural elements in the V3 crown of HIV-1 gp120. Nat Struct Mol Biol (2010) 1.63
Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. Proc Natl Acad Sci U S A (1993) 1.52
Human immunodeficiency virus type 2. J Gen Virol (2002) 1.50
Structural classification of CDR-H3 in antibodies. FEBS Lett (1996) 1.43
Crystal structure of the principal neutralization site of HIV-1. Science (1994) 1.43
Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs. Structure (1999) 1.42
Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization. J Mol Biol (2007) 1.42
Variability of human immunodeficiency virus type 2 (hiv-2) infecting patients living in france. Virology (2001) 1.40
Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens. Structure (2009) 1.34
Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100. Cancer Res (2009) 1.26
Recurring conformation of the human immunodeficiency virus type 1 gp120 V3 loop. Virology (2003) 1.20
Preferred CDRH3 lengths for antibodies with defined specificities. Int Immunol (1998) 1.18
Induced fit in HIV-neutralizing antibody complexes: evidence for alternative conformations of the gp120 V3 loop and the molecular basis for broad neutralization. Biochemistry (2005) 1.16
Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition. J Mol Biol (1995) 1.15
In vivo genetic variability of the human immunodeficiency virus type 2 V3 region. J Virol (1992) 1.11
Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex. J Mol Biol (1993) 1.10
AS2TS system for protein structure modeling and analysis. Nucleic Acids Res (2005) 1.07
Present and future challenges and limitations in protein-protein docking. Proteins (2010) 1.02
Location, exposure, and conservation of neutralizing and nonneutralizing epitopes on human immunodeficiency virus type 2 SU glycoprotein. J Virol (1996) 0.98
Two neutralizing domains in the V3 region in the envelope glycoprotein gp125 of HIV type 2. J Immunol (1994) 0.96
Equilibrium between metarhodopsin-I and metarhodopsin-II is dependent on the conformation of the third cytoplasmic loop. J Biol Chem (2005) 0.89
Neutralizing monoclonal antibodies against human immunodeficiency virus type 2 gp120. J Virol (1995) 0.89
Comparison of CH1 domains in different classes of murine antibodies. J Mol Biol (1996) 0.82
Fine characterization of a V3-region neutralizing epitope in human immunodeficiency virus type 2. Virus Res (1999) 0.82
HIV-2 neutralization by intact V3-specific Fab fragments. Virol J (2008) 0.81
Deletion of the V1/V2 region does not increase the accessibility of the V3 region of recombinant gp125. Curr HIV Res (2006) 0.81
Genetic variability of human immunodeficiency virus type 2 C2V3 region within and between individuals from Bissau, Guinea-Bissau, West Africa. AIDS Res Hum Retroviruses (2000) 0.81
Structural insights into steroid hormone binding: the crystal structure of a recombinant anti-testosterone Fab fragment in free and testosterone-bound forms. J Biol Chem (2001) 0.77
Production, purification, crystallization and preliminary X-ray diffraction analysis of the HIV-2-neutralizing V3 loop-specific Fab fragment 7C8. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.76
A TLR4 polymorphism is associated with asthma and reduced lipopolysaccharide-induced interleukin-12(p70) responses in Swedish children. J Allergy Clin Immunol (2004) 2.12
Differential susceptibility to human immunodeficiency virus type 1 infection of myeloid and plasmacytoid dendritic cells. J Virol (2005) 1.97
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput (2012) 1.93
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA. J Comput Chem (2011) 1.81
A signal peptide derived from hsp60 binds HLA-E and interferes with CD94/NKG2A recognition. J Exp Med (2002) 1.67
Molecular dynamics simulations of nucleic acid-protein complexes. Curr Opin Struct Biol (2008) 1.61
Mycoredoxin-1 is one of the missing links in the oxidative stress defence mechanism of Mycobacteria. Mol Microbiol (2012) 1.61
Molecular dynamics applied to nucleic acids. Acc Chem Res (2002) 1.52
Decreased plasma CXCL16/SR-PSOX concentration is associated with coronary artery disease. Atherosclerosis (2005) 1.52
Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition. J Immunol (2004) 1.46
HIV-1-infected dendritic cells up-regulate cell surface markers but fail to produce IL-12 p70 in response to CD40 ligand stimulation. Blood (2004) 1.42
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys J (2002) 1.40
Nimotuzumab, an antitumor antibody that targets the epidermal growth factor receptor, blocks ligand binding while permitting the active receptor conformation. Cancer Res (2009) 1.40
[The campaign for TBE vaccination of small children is unethical and incorrect]. Lakartidningen (2004) 1.39
Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100. Cancer Res (2009) 1.26
Crystal structure of plant pectin methylesterase. FEBS Lett (2002) 1.20
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res (2006) 1.12
The crystal structure of the major cat allergen Fel d 1, a member of the secretoglobin family. J Biol Chem (2003) 1.11
Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization. Biophys J (2005) 1.11
The glutaredoxin -C-P-Y-C- motif: influence of peripheral residues. Structure (2004) 1.11
Structure-function defects of the TWINKLE linker region in progressive external ophthalmoplegia. J Mol Biol (2008) 1.11
Low levels of perforin expression in CD8+ T lymphocyte granules in lymphoid tissue during acute human immunodeficiency virus type 1 infection. J Infect Dis (2002) 1.10
Presence of Rickettsia helvetica in granulomatous tissue from patients with sarcoidosis. J Infect Dis (2002) 1.10
IgG regulates the CD1 expression profile and lipid antigen-presenting function in human dendritic cells via FcgammaRIIa. Blood (2008) 1.10
Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase. Nature (2007) 1.09
Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides. J Phys Chem B (2005) 1.08
Subway particles are more genotoxic than street particles and induce oxidative stress in cultured human lung cells. Chem Res Toxicol (2005) 1.06
Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus. Hum Mutat (2004) 1.06
Circulating matrix metalloproteinase-9 is associated with cardiovascular risk factors in a middle-aged normal population. PLoS One (2008) 1.06
Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics. Biophys J (2006) 1.05
Two crystal structures of pneumococcal pilus sortase C provide novel insights into catalysis and substrate specificity. J Mol Biol (2009) 1.05
Primary HIV-1 R5 isolates from end-stage disease display enhanced viral fitness in parallel with increased gp120 net charge. Virology (2008) 1.04
Structure-function defects of the twinkle amino-terminal region in progressive external ophthalmoplegia. Biochim Biophys Acta (2008) 1.02
Crystal structure of the dog lipocalin allergen Can f 2: implications for cross-reactivity to the cat allergen Fel d 4. J Mol Biol (2010) 1.02
Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comput Chem (2002) 1.01
Immunogenicity and tolerability of a heptavalent pneumococcal conjugate vaccine administered at 3, 5 and 12 months of age. Pediatr Infect Dis J (2005) 1.00
Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. RNA (2005) 1.00
Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Res (2008) 1.00
Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study. Nucleic Acids Res (2008) 0.99
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations. Biophys J (2003) 0.98
Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity. Proteins (2009) 0.97
Natural killer cell tolerance persists despite significant reduction of self MHC class I on normal target cells in mice. PLoS One (2010) 0.96
Plasmodium falciparum rosetting epitopes converge in the SD3-loop of PfEMP1-DBL1α. PLoS One (2012) 0.95
Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA (2011) 0.94
Horizontal transfer of DNA by the uptake of apoptotic bodies. Vox Sang (2002) 0.94
How thioredoxin dissociates its mixed disulfide. PLoS Comput Biol (2009) 0.94
Triggering of dendritic cell responses after exposure to activated, but not resting, apoptotic PBMCs. J Immunol (2007) 0.94
Structural characterization of the tetrameric form of the major cat allergen Fel d 1. J Mol Biol (2007) 0.93
Active site residues controlling substrate specificity in 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42. J Ind Microbiol Biotechnol (2005) 0.92
Advances in biomolecular simulations: methodology and recent applications. Q Rev Biophys (2003) 0.92
Captopril potentiates the anticonvulsant activity of carbamazepine and lamotrigine in the mouse maximal electroshock seizure model. J Neural Transm (Vienna) (2010) 0.92
Proinflammatory and type 1 cytokine expression in cervical mucosa during HIV-1 and human papillomavirus infection. J Acquir Immune Defic Syndr (2007) 0.91
Unfolding of the amyloid β-peptide central helix: mechanistic insights from molecular dynamics simulations. PLoS One (2011) 0.91
Assessment of mucosal immunity to HIV-1. Expert Rev Vaccines (2010) 0.91
Malondialdehyde modification of myelin oligodendrocyte glycoprotein leads to increased immunogenicity and encephalitogenicity. Eur J Immunol (2007) 0.91
Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA (2013) 0.91
Fatty acids derived from royal jelly are modulators of estrogen receptor functions. PLoS One (2010) 0.90
Plasma levels of matrix metalloproteinase-9 are independently associated with psychosocial factors in a middle-aged normal population. Psychosom Med (2009) 0.90
Asthma, lung function and allergy in 12-year-old children with very low birth weight: a prospective study. Pediatr Allergy Immunol (2003) 0.90
Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae. MBio (2014) 0.90
Does the dynamic Stokes shift report on slow protein hydration dynamics? J Phys Chem B (2009) 0.89
Should fimbriae be included in pertussis vaccines? Studies on ELISA IgG anti-Fim2/3 antibodies after vaccination and infection. APMIS (2009) 0.89
Exogenous Nef is an inhibitor of Mycobacterium tuberculosis-induced tumor necrosis factor-alpha production and macrophage apoptosis. J Biol Chem (2010) 0.88
Thermal unfolding simulations of a multimeric protein--transition state and unfolding pathways. Proteins (2005) 0.87
Maternal MHC regulates generation of pathogenic antibodies and fetal MHC-encoded genes determine susceptibility in congenital heart block. J Immunol (2010) 0.87
Effect of Zn2+ on DNA recognition and stability of the p53 DNA-binding domain. Biochemistry (2006) 0.87
NK cell apoptosis in coronary artery disease: relation to oxidative stress. Atherosclerosis (2008) 0.86
Human cytomegalovirus-derived protein UL18 alters the phenotype and function of monocyte-derived dendritic cells. J Leukoc Biol (2007) 0.86
Bone mineral density and bone turnover in relation to serum leptin, alpha-ketoglutarate and sex steroids in overweight and obese postmenopausal women. Clin Endocrinol (Oxf) (2008) 0.86
Loss of the p21(Cip1/Waf1) cyclin kinase inhibitor results in propagation of horizontally transferred DNA. Cancer Res (2002) 0.86
Production, crystallization and preliminary crystallographic study of the major cat allergen Fel d 1. Acta Crystallogr D Biol Crystallogr (2003) 0.86
Spontaneous mutations in the human CMV HLA class I homologue UL18 affect its binding to the inhibitory receptor LIR-1/ILT2/CD85j. Eur J Immunol (2006) 0.86
Site-directed mutations at D1-Thr179 of photosystem II in Synechocystis sp. PCC 6803 modify the spectroscopic properties of the accessory chlorophyll in the D1-branch of the reaction center. Biochemistry (2008) 0.85
Diverse foxp3 expression in children with type 1 diabetes and celiac disease. Ann N Y Acad Sci (2008) 0.85
Stabilization of the catalytic thiolate in a mammalian glutaredoxin: structure, dynamics and electrostatics of reduced pig glutaredoxin and its mutants. J Mol Biol (2007) 0.85
Determining Rieske cluster reduction potentials. J Biol Inorg Chem (2008) 0.85
Plasminogen activator inhibitor-1 4G/5G polymorphism and risk of stroke: replicated findings in two nested case-control studies based on independent cohorts. Stroke (2005) 0.85
A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity. J Biol Chem (2005) 0.85
The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold. Open Biol (2014) 0.85
TAP-independent self-peptides enhance T cell recognition of immune-escaped tumors. J Clin Invest (2016) 0.85
Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins (2008) 0.84
IFN-α induces APOBEC3G, F, and A in immature dendritic cells and limits HIV-1 spread to CD4+ T cells. J Immunol (2013) 0.84
Proline substitution independently enhances H-2D(b) complex stabilization and TCR recognition of melanoma-associated peptides. Eur J Immunol (2013) 0.84
Isobolographic characterization of interactions of retigabine with carbamazepine, lamotrigine, and valproate in the mouse maximal electroshock-induced seizure model. Naunyn Schmiedebergs Arch Pharmacol (2008) 0.84
Glucocorticoid receptor point mutation V571M facilitates coactivator and ligand binding by structural rearrangement and stabilization. Mol Endocrinol (2005) 0.84
Allergen-induced cytokine secretion in atopic and non-atopic asthmatic children. Pediatr Allergy Immunol (2003) 0.83
Multiple polymorphisms affect expression and function of the neuropeptide S receptor (NPSR1). PLoS One (2011) 0.83
Class I major histocompatibility complex, the trojan horse for secretion of amyloidogenic β2-microglobulin. J Biol Chem (2013) 0.83
Increased sensitivity to broadly neutralizing antibodies of end-stage disease R5 HIV-1 correlates with evolution in Env glycosylation and charge. PLoS One (2011) 0.83
Immune modulation by the human cytomegalovirus-encoded molecule UL18, a mystery yet to be solved. J Immunol (2008) 0.83
Early rapid weight gain and current overweight in relation to asthma in adolescents born with very low birth weight. Pediatr Allergy Immunol (2005) 0.83
The -Cys-X1-X2-Cys- motif of reduced glutaredoxins adopts a consensus structure that explains the low pK(a) of its catalytic cysteine. Biochemistry (2012) 0.82
The reducing activity of glutaredoxin 3 toward cytoplasmic substrate proteins is restricted by methionine 43. Biochemistry (2007) 0.82
NK cell inhibitory receptor Ly-49C residues involved in MHC class I binding. J Immunol (2002) 0.82
Reduced serum levels of autoantibodies against monomeric C-reactive protein (CRP) in patients with acute coronary syndrome. Clin Chim Acta (2008) 0.82
The role of residue 50 and hydration water molecules in homeodomain DNA recognition. Eur Biophys J (2002) 0.82
Immunogenicity and reactogenicity of two diphtheria-tetanus-acellular pertussis-hepatitis B-inactivated polio virus-Haemophilus influenzae type b vaccines administered at 3, 5 and 11-12 months of age. Hum Vaccin (2009) 0.81
Immunization with apoptotic pseudovirus transduced cells induces both cellular and humoral responses: a proof of concept study in macaques. Vaccine (2012) 0.81
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations. Proteins (2002) 0.81