Published in Virology on September 30, 2003
HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev (2008) 2.88
Coordinate linkage of HIV evolution reveals regions of immunological vulnerability. Proc Natl Acad Sci U S A (2011) 2.37
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PLoS Comput Biol (2007) 1.78
Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein. PLoS Genet (2016) 1.46
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc (2008) 1.43
Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol (2010) 1.39
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol (2009) 1.37
Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J (2010) 1.30
Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. AIDS Rev (2008) 1.26
The choreography of HIV-1 proteolytic processing and virion assembly. J Biol Chem (2012) 1.23
Novel human immunodeficiency virus type 1 protease mutations potentially involved in resistance to protease inhibitors. Antimicrob Agents Chemother (2005) 1.23
Why should we care about molecular coevolution? Evol Bioinform Online (2008) 1.19
Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins. J Virol (2007) 1.14
Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PLoS One (2010) 1.12
Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics (2008) 1.10
Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. PLoS Comput Biol (2010) 1.07
Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. J Virol (2006) 1.06
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinformatics (2009) 1.02
Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance. Protein Sci (2010) 1.01
New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors. Curr Opin HIV AIDS (2008) 0.96
Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. PLoS One (2007) 0.95
Interplay between single resistance-associated mutations in the HIV-1 protease and viral infectivity, protease activity, and inhibitor sensitivity. Antimicrob Agents Chemother (2011) 0.90
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics (2011) 0.89
Distinct resistance mutation and polymorphism acquisition in HIV-1 protease of subtypes B and F1 from children and adult patients under virological failure. Infect Genet Evol (2008) 0.89
Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors. PLoS One (2009) 0.87
Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. J Virol (2007) 0.85
Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor. AIDS (2009) 0.85
Co-lethality studied as an asset against viral drug escape: the HIV protease case. Biol Direct (2010) 0.84
Interrogating and predicting tolerated sequence diversity in protein folds: application to E. elaterium trypsin inhibitor-II cystine-knot miniprotein. PLoS Comput Biol (2009) 0.83
Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data. PLoS One (2013) 0.83
Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. PLoS Comput Biol (2015) 0.82
Correlated mutation analysis on the catalytic domains of serine/threonine protein kinases. PLoS One (2009) 0.81
Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Mol Biol Evol (2008) 0.81
Strong epistatic selection on the RNA secondary structure of HIV. PLoS Pathog (2014) 0.79
Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. Pac Symp Biocomput (2009) 0.79
Amino acid covariation in a functionally important human immunodeficiency virus type 1 protein region is associated with population subdivision. Genetics (2009) 0.79
Synthetic lethals in HIV: ways to avoid drug resistance : Running title: Preventing HIV resistance. Biol Direct (2015) 0.76
Alternative methods to analyse the impact of HIV mutations on virological response to antiviral therapy. BMC Med Res Methodol (2008) 0.76
CoVaMa: Co-Variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data. Methods (2015) 0.75
In Vivo validation of a bioinformatics based tool to identify reduced replication capacity in HIV-1. Open Med Inform J (2010) 0.75
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol (2017) 0.75
Data-intensive analysis of HIV mutations. BMC Bioinformatics (2015) 0.75
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A (2008) 16.54
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol (2008) 7.54
Architecture and secondary structure of an entire HIV-1 RNA genome. Nature (2009) 6.12
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A (2011) 4.68
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98
Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol (2004) 2.91
Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure (2002) 2.69
Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. J Med Chem (2005) 2.58
Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor. J Virol (2004) 2.47
Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chem Biol (2004) 2.39
Accuracy of the TRUGENE HIV-1 genotyping kit. J Clin Microbiol (2003) 2.32
Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. J Virol (2002) 2.19
Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest (2012) 2.05
Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates. AIDS (2007) 2.03
Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol (2002) 1.71
Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection. J Virol (2009) 1.70
Characterization and selection of HIV-1 subtype C isolates for use in vaccine development. AIDS Res Hum Retroviruses (2003) 1.68
Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia. PLoS Pathog (2009) 1.66
Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J Virol (2004) 1.65
Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces. Structure (2010) 1.65
Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proc Natl Acad Sci U S A (2010) 1.65
Increased human immunodeficiency virus type 1 (HIV-1) env compartmentalization in the presence of HIV-1-associated dementia. J Virol (2005) 1.65
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog (2011) 1.57
Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS (2004) 1.51
Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease. Protein Sci (2002) 1.49
Processing sites in the human immunodeficiency virus type 1 (HIV-1) Gag-Pro-Pol precursor are cleaved by the viral protease at different rates. Retrovirology (2005) 1.48
HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog (2010) 1.47
HIV-1 replication in the central nervous system occurs in two distinct cell types. PLoS Pathog (2011) 1.45
Turnover of env variable region 1 and 2 genotypes in subjects with late-stage human immunodeficiency virus type 1 infection. J Virol (2003) 1.44
HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc (2008) 1.43
The challenge of developing robust drugs to overcome resistance. Drug Discov Today (2011) 1.43
Alphavirus replicon particles as candidate HIV vaccines. IUBMB Life (2002) 1.41
Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course. AIDS (2009) 1.40
Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol (2010) 1.39
Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J Biol Chem (2012) 1.38
Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy. J Virol (2003) 1.37
Measuring allelic heterogeneity in Plasmodium falciparum by a heteroduplex tracking assay. Am J Trop Med Hyg (2005) 1.35
Role of low CD4 levels in the influence of human immunodeficiency virus type 1 envelope V1 and V2 regions on entry and spread in macrophages. J Virol (2005) 1.34
Correlation between env V1/V2 region diversification and neutralizing antibodies during primary infection by simian immunodeficiency virus sm in rhesus macaques. J Virol (2004) 1.32
Cross-sectional detection of acute HIV infection: timing of transmission, inflammation and antiretroviral therapy. PLoS One (2011) 1.32
The molecular basis of drug resistance against hepatitis C virus NS3/4A protease inhibitors. PLoS Pathog (2012) 1.30
A strongly transdominant mutation in the human immunodeficiency virus type 1 gag gene defines an Achilles heel in the virus life cycle. J Virol (2009) 1.30
First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem Biol (2012) 1.28
PTEN enters the nucleus by diffusion. J Cell Biochem (2005) 1.28
Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. AIDS Rev (2008) 1.26
The choreography of HIV-1 proteolytic processing and virion assembly. J Biol Chem (2012) 1.23
Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology (2006) 1.22
Compartmentalized human immunodeficiency virus type 1 present in cerebrospinal fluid is produced by short-lived cells. J Virol (2005) 1.22
Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure (2007) 1.20
Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses (2010) 1.20
Insights into interferon regulatory factor activation from the crystal structure of dimeric IRF5. Nat Struct Mol Biol (2008) 1.17
Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J Med Chem (2006) 1.17
Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. AIDS Res Hum Retroviruses (2007) 1.16
Genotypic susceptibility scores and HIV type 1 RNA responses in treatment-experienced subjects with HIV type 1 infection. AIDS Res Hum Retroviruses (2008) 1.15
Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol (2006) 1.15
A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia. J Infect Dis (2010) 1.15
Viral protease inhibitors. Handb Exp Pharmacol (2009) 1.14
Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. J Mol Biol (2011) 1.14
Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins. J Virol (2007) 1.14
Vaccination of macaques with SIV immunogens delivered by Venezuelan equine encephalitis virus replicon particle vectors followed by a mucosal challenge with SIVsmE660. Vaccine (2005) 1.14
Crystal structure of the DNA cytosine deaminase APOBEC3F: the catalytically active and HIV-1 Vif-binding domain. Structure (2013) 1.13
Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins (2003) 1.12
Therapeutic targeting of C-terminal binding protein in human cancer. Cell Cycle (2010) 1.12
Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des (2007) 1.12
Genetic characteristics of the V3 region associated with CXCR4 usage in HIV-1 subtype C isolates. Virology (2006) 1.12
HIV pathogenesis: dynamics and genetics of viral populations and infected cells. Cold Spring Harb Perspect Med (2013) 1.11
The genetic bottleneck in vertical transmission of subtype C HIV-1 is not driven by selection of especially neutralization-resistant virus from the maternal viral population. J Virol (2011) 1.10
Design of HIV-1 protease inhibitors active on multidrug-resistant virus. J Med Chem (2005) 1.10
Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. J Virol (2006) 1.10
Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs. PLoS Pathog (2013) 1.08
Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. J Virol (2009) 1.07
HIV-1 populations in blood and breast milk are similar. Virology (2004) 1.06
Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease. J Virol (2007) 1.06
Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease. J Virol (2011) 1.05
Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother (2006) 1.05
Evolution of the HIV-1 env gene in the Rag2-/- gammaC-/- humanized mouse model. J Virol (2009) 1.05
HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study. PLoS One (2013) 1.04
Quantification of entry phenotypes of macrophage-tropic HIV-1 across a wide range of CD4 densities. J Virol (2013) 1.04
Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity. Proteins (2007) 1.04
Dynamics of simian immunodeficiency virus populations in blood and cerebrospinal fluid over the full course of infection. J Infect Dis (2007) 1.02
Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV. J Chem Theory Comput (2010) 1.02
Selection of high-level resistance to human immunodeficiency virus type 1 protease inhibitors. Antimicrob Agents Chemother (2003) 1.02
A rev1-vpu polymorphism unique to HIV-1 subtype A and C strains impairs envelope glycoprotein expression from rev-vpu-env cassettes and reduces virion infectivity in pseudotyping assays. Virology (2009) 1.02
Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol (2013) 1.01
Point mutants of EHEC intimin that diminish Tir recognition and actin pedestal formation highlight a putative Tir binding pocket. Mol Microbiol (2002) 1.01
Independent evolution of human immunodeficiency virus type 1 env V1/V2 and V4/V5 hypervariable regions during chronic infection. J Virol (2007) 1.01
Central nervous system compartmentalization of HIV-1 subtype C variants early and late in infection in young children. PLoS Pathog (2012) 1.01
Contribution of Ser386 and Ser396 to activation of interferon regulatory factor 3. J Mol Biol (2008) 1.00
The molecular epidemiology of HIV-1 envelope diversity during HIV-1 subtype C vertical transmission in Malawian mother-infant pairs. AIDS (2008) 0.99
The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways. J Virol (2010) 0.99
Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins (2008) 0.99
CAPRISA 004 tenofovir microbicide trial: no impact of tenofovir gel on the HIV transmission bottleneck. J Infect Dis (2012) 0.99
Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J Am Chem Soc (2012) 0.99
Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput (2012) 0.98