Published in Proc Natl Acad Sci U S A on December 18, 2001
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model (2010) 3.04
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci (2002) 1.54
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. J Comput Chem (2010) 1.41
Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses (2010) 1.20
Molecular dynamics reveal BCR-ABL1 polymutants as a unique mechanism of resistance to PAN-BCR-ABL1 kinase inhibitor therapy. Proc Natl Acad Sci U S A (2014) 1.16
Predicting drug resistance of the HIV-1 protease using molecular interaction energy components. Proteins (2009) 1.07
Diarylaniline derivatives as a distinct class of HIV-1 non-nucleoside reverse transcriptase inhibitors. J Med Chem (2010) 1.06
Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV. J Chem Theory Comput (2010) 1.02
Cellular interaction through LewisX cluster: theoretical studies. J Mol Model (2008) 0.99
Evaluating the potency of HIV-1 protease drugs to combat resistance. Proteins (2008) 0.97
Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase. Biophys J (2008) 0.97
Structure-based methods for predicting target mutation-induced drug resistance and rational drug design to overcome the problem. Drug Discov Today (2012) 0.93
Interaction of I50V mutant and I50L/A71V double mutant HIV-protease with inhibitor TMC114 (darunavir): molecular dynamics simulation and binding free energy studies. J Phys Chem B (2012) 0.89
Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy. J Phys Chem B (2011) 0.88
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. J Comput Aided Mol Des (2012) 0.88
Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir. J Mol Model (2004) 0.88
Novel method for probing the specificity binding profile of ligands: applications to HIV protease. Chem Biol Drug Des (2008) 0.87
Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase. PLoS Comput Biol (2009) 0.87
Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrob Agents Chemother (2004) 0.87
Structure-based phenotyping predicts HIV-1 protease inhibitor resistance. Protein Sci (2003) 0.86
Dynamical basis for drug resistance of HIV-1 protease. BMC Struct Biol (2011) 0.85
Inhibition of nutlin-resistant HDM2 mutants by stapled peptides. PLoS One (2013) 0.85
A computational analysis of the binding model of MDM2 with inhibitors. J Comput Aided Mol Des (2010) 0.85
Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys J (2010) 0.85
The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations. J Comput Aided Mol Des (2011) 0.85
Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry (2010) 0.83
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure (2009) 0.83
Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation. J Mol Model (2009) 0.82
Validating the vitality strategy for fighting drug resistance. Proteins (2012) 0.81
Decomposing the energetic impact of drug-resistant mutations: the example of HIV-1 protease-DRV binding. Methods Mol Biol (2012) 0.80
Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation. J Mol Model (2014) 0.80
Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA. PLoS One (2014) 0.78
Multiscale generalized born modeling of ligand binding energies for virtual database screening. J Phys Chem B (2009) 0.78
Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations. J Mol Model (2011) 0.77
Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA. PLoS One (2015) 0.77
In silico prediction of mutant HIV-1 proteases cleaving a target sequence. PLoS One (2014) 0.76
Structural basis for decreased affinity of Emodin binding to Val66-mutated human CK2 alpha as determined by molecular dynamics. J Mol Model (2009) 0.76
Impact of rtI233V mutation in hepatitis B virus polymerase protein and adefovir efficacy: Homology modeling and molecular docking studies. Bioinformation (2013) 0.76
Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism. J Mol Graph Model (2014) 0.76
Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides. J Zhejiang Univ Sci B (2015) 0.75
Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods. PLoS One (2015) 0.75
Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). PLoS Comput Biol (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res (2000) 10.78
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Structure-based inhibitors of HIV-1 protease. Annu Rev Biochem (1993) 4.80
Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct (1998) 3.48
Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure. Biochemistry (1995) 2.90
How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol (2000) 2.62
Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959. Virology (1995) 2.29
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
Structural mechanisms of HIV drug resistance. Annu Rev Pharmacol Toxicol (1996) 1.79
The not-so-great escape. Nat Struct Biol (1995) 1.77
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. Proc Natl Acad Sci U S A (1999) 1.56
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J Mol Biol (2000) 1.46
Resistance to HIV protease inhibitors: a comparison of enzyme inhibition and antiviral potency. Biochemistry (1998) 1.43
Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J Biol Chem (1996) 1.39
X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Natl Acad Sci U S A (1990) 1.34
Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes? J Mol Biol (1998) 1.31
Non-functional conserved residues in globins and their possible role as a folding nucleus. J Mol Biol (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
Kinetic properties of saquinavir-resistant mutants of human immunodeficiency virus type 1 protease and their implications in drug resistance in vivo. Biochemistry (1997) 1.20
Inhibition of HIV protease activity by heterodimer formation. Biochemistry (1991) 1.15
Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation. Proc Natl Acad Sci U S A (1996) 0.97
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
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
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
Electrostatic potentials of proteins. 1. Carboxypeptidase A. J Am Chem Soc (1976) 0.90
An analysis of current methodologies for conformational searching of complex molecules. J Med Chem (1988) 0.90
Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. Biophys J (2001) 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
Why do A.T base pairs inhibit Z-DNA formation? Proc Natl Acad Sci U S A (1990) 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
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
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
Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. J Biomol NMR (1999) 0.85
Molecular mechanics simulations on covalent complexes between anthramycin and B DNA. J Med Chem (1986) 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
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
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
Stabilizing and destabilizing effects of placing beta-branched amino acids in protein alpha-helices. Biochemistry (1994) 0.83
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
An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates. Biochim Biophys Acta (1980) 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
Free energy component analysis: application to the "Z-phobicity" of A-T base pairs. J Biomol Struct Dyn (1993) 0.82
Molecular orbital studies of thyroid hormone analogs. J Am Chem Soc (1973) 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
Electrostatic potentials of deoxydinucleoside monophosphates. 1. Deoxydinucleoside monophosphates and actinomycin chromophore interactions. J Med Chem (1979) 0.81
Effects of nucleotide bromination on the stabilities of Z-RNA and Z-DNA: a molecular mechanics/thermodynamic perturbation study. Biopolymers (1989) 0.81