Published in Nucleic Acids Res on December 15, 2000
Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophys J (2008) 1.24
The bulge region of HIV-1 TAR RNA binds metal ions in solution. Nucleic Acids Res (2002) 1.08
Analyzing the flexibility of RNA structures by constraint counting. Biophys J (2008) 1.07
iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. Biophys J (2007) 1.01
Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer. Nucleic Acids Res (2003) 0.97
Evidence for a base triple in the free HIV-1 TAR RNA. RNA (2004) 0.91
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys J (2001) 0.90
Inhibition of Tat-mediated HIV-1 replication and neurotoxicity by novel GSK3-beta inhibitors. Virology (2011) 0.88
Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study. Biophys J (2005) 0.86
Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain. Nucleic Acids Res (2002) 0.83
Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A (2016) 0.77
Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol (2017) 0.75
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science (1992) 5.08
Fragments of the HIV-1 Tat protein specifically bind TAR RNA. Science (1990) 4.33
Arginine-mediated RNA recognition: the arginine fork. Science (1991) 3.89
RNA recognition by Tat-derived peptides: interaction in the major groove? Cell (1991) 3.83
The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J Mol Biol (1995) 2.93
Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res (1996) 2.55
Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem Biol (1995) 2.51
High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region. J Mol Biol (1993) 2.44
Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science (1995) 2.35
Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J Mol Biol (1994) 2.27
An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng (1997) 2.17
Role of RNA structure in arginine recognition of TAR RNA. Proc Natl Acad Sci U S A (1993) 1.94
Specific binding of arginine to TAR RNA. Proc Natl Acad Sci U S A (1992) 1.90
Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease. J Mol Biol (1994) 1.75
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci U S A (1999) 1.56
A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc Natl Acad Sci U S A (1998) 1.50
Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J Biomol Struct Dyn (1998) 1.48
Solution structure of the HIV-2 TAR-argininamide complex. J Mol Biol (1997) 1.44
Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn (1998) 1.43
Conserved nucleotides in the TAR RNA stem of human immunodeficiency virus type 1 are critical for Tat binding and trans activation: model for TAR RNA tertiary structure. J Virol (1992) 1.43
The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc Natl Acad Sci U S A (1995) 1.38
Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA. Biochemistry (1999) 1.34
Electrostatic fields in antibodies and antibody/antigen complexes. Prog Biophys Mol Biol (1992) 1.31
Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol (2000) 1.31
Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA. Biochemistry (1995) 1.30
Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element. J Mol Biol (1992) 1.24
Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins. Nucleic Acids Res (1994) 1.21
Molecular dynamics investigations of hammerhead ribozyme RNA. Eur Biophys J (1998) 1.12
Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution. Biophys J (1999) 1.12
Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J Mol Biol (1997) 1.09
Electrostatic interactions in hirudin-thrombin binding. Biophys Chem (1996) 1.09
Simulations of the dynamics at an RNA-protein interface. Nat Struct Biol (1999) 1.08
Molecular dynamics studies of U1A-RNA complexes. RNA (1999) 1.08
NMR evidence for a base triple in the HIV-2 TAR C-G.C+ mutant-argininamide complex. Nucleic Acids Res (1998) 1.05
Investigating the binding specificity of U1A-RNA by computational mutagenesis. J Mol Biol (2000) 1.02
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (1998) 8.46
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn (1999) 5.14
The maximal affinity of ligands. Proc Natl Acad Sci U S A (1999) 3.24
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J Mol Biol (1996) 2.66
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc (2001) 2.55
Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature (1984) 2.36
Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem (2000) 2.21
Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins (1993) 2.13
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct (2001) 2.06
Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (1987) 2.04
Free energy calculations by computer simulation. Science (1987) 1.98
Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem (2000) 1.92
On loop folding in nucleic acid hairpin-type structures. J Biomol Struct Dyn (1986) 1.85
Molecular dynamics in the endgame of protein structure prediction. J Mol Biol (2001) 1.69
Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers. Biopolymers (1981) 1.66
On low-barrier hydrogen bonds and enzyme catalysis. Science (1995) 1.60
Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. Proc Natl Acad Sci U S A (2001) 1.58
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci U S A (1999) 1.56
Electrostatic potential molecular surfaces. Proc Natl Acad Sci U S A (1982) 1.53
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Sci (1999) 1.51
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci U S A (1998) 1.49
Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J Biomol Struct Dyn (1998) 1.48
A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers (1991) 1.47
A molecular dynamics simulation of double-helical B-DNA including counterions and water. Proc Natl Acad Sci U S A (1985) 1.47
Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins (2000) 1.46
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J Mol Biol (2000) 1.46
Continuum solvent studies of the stability of RNA hairpin loops and helices. J Biomol Struct Dyn (1998) 1.43
Probing protein stability with unnatural amino acids. Science (1992) 1.42
Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin. Drug Metab Dispos (2000) 1.40
Protein model structure evaluation using the solvation free energy of folding. Proc Natl Acad Sci U S A (1990) 1.38
Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin. Nature (1987) 1.33
Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol (2000) 1.31
What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc Natl Acad Sci U S A (1993) 1.31
Molecular-mechanical studies of the mismatched base analogs of d(CGCGAATTCGCG)2:d(CGTGAATTCGCG)2, d(CGAGAATTCGCG)2, d(CGCGAATTCACG)2, d(CGCGAATTCTCG)2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG). Biopolymers (1984) 1.30
Calculation of protein tertiary structure. J Mol Biol (1976) 1.27
2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. J Am Chem Soc (2001) 1.25
A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc Natl Acad Sci U S A (1997) 1.23
Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings. Proc Natl Acad Sci U S A (1982) 1.23
What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins (1999) 1.21
An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. J Am Chem Soc (2001) 1.21
Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. J Mol Biol (1991) 1.19
Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study. Proteins (1999) 1.16
Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd. Biophys J (2001) 1.14
Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers (1991) 1.14
Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins (1989) 1.10
Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. Protein Sci (1992) 1.10
Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J Mol Biol (1997) 1.09
Molecular dynamics studies of U1A-RNA complexes. RNA (1999) 1.08
Computational studies of the interaction of myoglobin and xenon. J Mol Biol (1986) 1.08
Electrostatic potentials of proteins. 2. Role of electrostatics in a possible catalytic mechanism for carboxypeptidase A. J Am Chem Soc (1976) 1.07
The nature of enzyme catalysis in trypsin. Proc Natl Acad Sci U S A (1986) 1.05
The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"? Proteins (1996) 1.03
Investigating the binding specificity of U1A-RNA by computational mutagenesis. J Mol Biol (2000) 1.02
Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Proteins (2000) 1.02
Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. J Mol Biol (1988) 1.02
Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA. Biopolymers (1984) 1.01
Molecular mechanical studies of proflavine and acridine orange intercalation. Nucleic Acids Res (1981) 1.00
Nature of steroid-glucocorticoid receptor interactions: thermodynamic analysis of the binding reaction. Biochemistry (1978) 1.00
Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. Structure (2001) 0.98
Flexible ligand docking: a multistep strategy approach. Proteins (1999) 0.97
Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease. J Med Chem (1991) 0.96
Free energy calculation on base specificity of drug--DNA interactions: application to daunomycin and acridine intercalation into DNA. Biopolymers (1990) 0.96
Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment. Proc Natl Acad Sci U S A (1994) 0.96
Seroepidemiology of hepatitis B virus in the Philippines. Am J Epidemiol (1986) 0.95
An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. J Am Chem Soc (2001) 0.95
Computed free energy differences between point mutations in a collagen-like peptide. Biopolymers (2001) 0.94
Modeling protein stability: a theoretical analysis of the stability of T4 lysozyme mutants. Protein Eng (1997) 0.92
A diffusion--collision--adhesion model for the kinetics of myoglobin refolding. Nature (1980) 0.91
Free energy calculations of the mutation of Ile96-->Ala in barnase: contributions to the difference in stability. Protein Eng (1996) 0.91
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys J (2001) 0.90
An analysis of current methodologies for conformational searching of complex molecules. J Med Chem (1988) 0.90
Electrostatic potentials of proteins. 1. Carboxypeptidase A. J Am Chem Soc (1976) 0.90
Computational analysis of structural and energetic consequences of DNA methylation. Carcinogenesis (1989) 0.89
The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin. Biophys J (2006) 0.89
Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case. Protein Sci (1992) 0.88
Understanding the thermodynamic stability of an RNA hairpin and its mutant. Biophys J (1996) 0.88
Molecular mechanical studies of d(CGTACG)2: complex of triostin A with the middle A - T base pairs in either Hoogsteen or Watson-Crick pairing. Proc Natl Acad Sci U S A (1986) 0.86
Can one predict protein stability? An attempt to do so for residue 133 of T4 lysozyme using a combination of free energy derivatives, PROFEC, and free energy perturbation methods. Proteins (1998) 0.86
Why do A.T base pairs inhibit Z-DNA formation? Proc Natl Acad Sci U S A (1990) 0.86
A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA. Protein Sci (1994) 0.85
Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations. J Med Chem (1999) 0.85
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. J Biomol NMR (1999) 0.85
Calculation and prediction of binding free energies for the matrix metalloproteinases. J Med Chem (2000) 0.85
Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol (1990) 0.85
Molecular mechanics simulations on covalent complexes between anthramycin and B DNA. J Med Chem (1986) 0.84
The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors. J Comput Aided Mol Des (1998) 0.84
Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates. Antisense Res Dev (1991) 0.84
Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics. Biophys J (1997) 0.84
Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. J Biomol Struct Dyn (1994) 0.84
Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices. Biochemistry (1994) 0.83
Conformations of deoxydodecanucleotides with pyrimidine (6-4)-pyrimidone photoadducts. Photochem Photobiol (1985) 0.83
A model for thyroid hormone--receptor interactions. J Med Chem (1979) 0.83
Free energy component analysis: application to the "Z-phobicity" of A-T base pairs. J Biomol Struct Dyn (1993) 0.82
An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates. Biochim Biophys Acta (1980) 0.82
Molecular orbital studies of thyroid hormone analogs. J Am Chem Soc (1973) 0.82
Conformations of duplex structures formed by oligodeoxynucleotides covalently linked to the intercalator 2-methoxy-6-chloro-9-aminoacridine. J Biomol Struct Dyn (1987) 0.82
Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. J Med Chem (2001) 0.82
Molecular mechanical simulations on double intercalation of 9-amino acridine into d(CGCGCGC) X d(GCGCGCG): analysis of the physical basis for the neighbor-exclusion principle. Proc Natl Acad Sci U S A (1987) 0.82