Published in Structure on October 01, 2001
Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res (2005) 2.45
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics (2003) 1.24
Structure and dynamics of zymogen human blood coagulation factor X. Biophys J (2002) 1.05
X-ray vs. NMR structures as templates for computational protein design. Proteins (2009) 0.95
Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci (2005) 0.91
Distributions in protein conformation space: implications for structure prediction and entropy. Biophys J (2004) 0.85
Importance of dispersion and electron correlation in ab initio protein folding. J Phys Chem B (2009) 0.84
Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures. J Chem Theory Comput (2007) 0.82
Algorithmic approaches to protein-protein interaction site prediction. Algorithms Mol Biol (2015) 0.81
Smoothing protein energy landscapes by integrating folding models with structure prediction. Biophys J (2011) 0.75
Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins (2015) 0.75
Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-Based Scoring Functions. J Chem Theory Comput (2017) 0.75
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
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
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
Free energy calculation on base specificity of drug--DNA interactions: application to daunomycin and acridine intercalation into DNA. Biopolymers (1990) 0.96
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide. Nucleic Acids Res (2000) 0.96
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
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
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
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
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
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. J Biomol NMR (1999) 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
Calculation and prediction of binding free energies for the matrix metalloproteinases. J Med Chem (2000) 0.85
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
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 mechanics simulations on covalent complexes between anthramycin and B DNA. J Med Chem (1986) 0.84
Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain. J Biomol Struct Dyn (1994) 0.84
Application of free-energy decomposition to determine the relative stability of R and S oligodeoxyribonucleotide methylphosphonates. Antisense Res Dev (1991) 0.84
A model for thyroid hormone--receptor interactions. J Med Chem (1979) 0.83
Conformations of deoxydodecanucleotides with pyrimidine (6-4)-pyrimidone photoadducts. Photochem Photobiol (1985) 0.83
Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices. Biochemistry (1994) 0.83
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
An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates. Biochim Biophys Acta (1980) 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
Free energy component analysis: application to the "Z-phobicity" of A-T base pairs. J Biomol Struct Dyn (1993) 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
Effects of nucleotide bromination on the stabilities of Z-RNA and Z-DNA: a molecular mechanics/thermodynamic perturbation study. Biopolymers (1989) 0.81
Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions. J Med Chem (1979) 0.81