Published in Proteins on August 01, 2007
Structures of influenza A proteins and insights into antiviral drug targets. Nat Struct Mol Biol (2010) 2.31
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
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
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
HIV-1 Protease: Structural Perspectives on Drug Resistance. Viruses (2009) 1.37
Fragment-based screen against HIV protease. Chem Biol Drug Des (2010) 1.26
Molecular Basis for Drug Resistance in HIV-1 Protease. Viruses (2010) 1.20
Rational approaches to improving selectivity in drug design. J Med Chem (2012) 1.16
Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. J Mol Biol (2011) 1.14
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
Additivity in the analysis and design of HIV protease inhibitors. J Med Chem (2009) 0.95
Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study. BMC Bioinformatics (2011) 0.86
Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure (2009) 0.83
Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov (2009) 0.82
Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chem Biol Drug Des (2009) 0.82
Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol (2013) 0.81
Winning the arms race by improving drug discovery against mutating targets. ACS Chem Biol (2011) 0.81
Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol (2017) 0.75
Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition. Proteins (2015) 0.75
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res (2006) 10.36
Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A (2007) 4.33
Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem (2002) 3.43
Virtual screening of molecular databases using a support vector machine. J Chem Inf Model (2005) 2.40
Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. J Am Chem Soc (2004) 2.36
Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys (2007) 1.99
Theory of free energy and entropy in noncovalent binding. Chem Rev (2009) 1.96
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proc Natl Acad Sci U S A (2007) 1.87
Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys J (2004) 1.79
The Binding Database: data management and interface design. Bioinformatics (2002) 1.60
Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J Chem Phys (2012) 1.47
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
Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc (2009) 1.38
Tork: Conformational analysis method for molecules and complexes. J Comput Chem (2003) 1.35
Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comput Chem (2008) 1.35
Solution structure and functional ligand screening of HI0719, a highly conserved protein from bacteria to humans in the YjgF/YER057c/UK114 family. Biochemistry (2003) 1.30
SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res (2011) 1.29
Escherichia coli cell surface perturbation and disruption induced by antimicrobial peptides BP100 and pepR. J Biol Chem (2010) 1.27
New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. J Am Chem Soc (2011) 1.27
Configurational entropy in protein-peptide binding: computational study of Tsg101 ubiquitin E2 variant domain with an HIV-derived PTAP nonapeptide. J Mol Biol (2009) 1.26
Identification of symmetries in molecules and complexes. J Chem Inf Comput Sci (2004) 1.24
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des (2012) 1.23
Public domain databases for medicinal chemistry. J Med Chem (2012) 1.23
Screening drug-like compounds by docking to homology models: a systematic study. J Chem Inf Model (2006) 1.23
The SAMPL4 host-guest blind prediction challenge: an overview. J Comput Aided Mol Des (2014) 1.20
Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility. J Comput Chem (2002) 1.19
Concepts in receptor optimization: targeting the RGD peptide. J Am Chem Soc (2006) 1.15
Viral protease inhibitors. Handb Exp Pharmacol (2009) 1.14
Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des (2007) 1.12
Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci U S A (2012) 1.12
Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry (2003) 1.10
Three residues in HIV-1 matrix contribute to protease inhibitor susceptibility and replication capacity. Antimicrob Agents Chemother (2010) 1.09
On the theory of noncovalent binding. Biophys J (2004) 1.01
Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model. J Chem Theory Comput (2012) 0.96
Additivity in the analysis and design of HIV protease inhibitors. J Med Chem (2009) 0.95
The carmaphycins: new proteasome inhibitors exhibiting an α,β-epoxyketone warhead from a marine cyanobacterium. Chembiochem (2012) 0.95
Modeling Protein-Ligand Binding by Mining Minima. J Chem Theory Comput (2010) 0.92
Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations. J Biomol NMR (2004) 0.91
Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields. J Comput Aided Mol Des (2012) 0.90
Lipid membrane-induced optimization for ligand-receptor docking: recent tools and insights for the "membrane catalysis" model. Eur Biophys J (2005) 0.90
Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. J Comput Chem (2013) 0.89
Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA. Proteomics (2012) 0.89
Dual inhibitors of P-glycoprotein and tumor cell growth: (re)discovering thioxanthones. Biochem Pharmacol (2011) 0.87
Discovery of a new small-molecule inhibitor of p53-MDM2 interaction using a yeast-based approach. Biochem Pharmacol (2013) 0.87
Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re(I) bipyridine catalysts at a lower overpotential. J Am Chem Soc (2014) 0.86
Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput (2015) 0.86
Sampling conformations in high dimensions using low-dimensional distribution functions. J Chem Phys (2009) 0.85
Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc (2014) 0.85
Sulfated small molecules targeting eBV in Burkitt lymphoma: from in silico screening to the evidence of in vitro effect on viral episomal DNA. Chem Biol Drug Des (2013) 0.85
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations. J Comput Aided Mol Des (2014) 0.84
The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling. J Chem Phys (2013) 0.84
Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. Biophys J (2009) 0.83
New uses for old drugs: pharmacophore-based screening for the discovery of P-glycoprotein inhibitors. Chem Biol Drug Des (2011) 0.83
Insights into the in vitro antitumor mechanism of action of a new pyranoxanthone. Chem Biol Drug Des (2010) 0.82
Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chem Biol Drug Des (2009) 0.82
Structural and functional analysis of rare missense mutations in human chorionic gonadotrophin β-subunit. Mol Hum Reprod (2012) 0.82
Structure and ligand-based design of P-glycoprotein inhibitors: a historical perspective. Curr Pharm Des (2012) 0.81
Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. J Antimicrob Chemother (2012) 0.81
The Fundamental Role of Flexibility on the Strength of Molecular Binding. Soft Matter (2012) 0.81
Structural model for an AxxxG-mediated dimer of surfactant-associated protein C. Eur J Biochem (2004) 0.81
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J Comput Aided Mol Des (2014) 0.81
ConCept: de novo design of synthetic receptors for targeted ligands. J Chem Inf Model (2007) 0.81
Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems. J Chem Theory Comput (2012) 0.80
Correlation as a determinant of configurational entropy in supramolecular and protein systems. J Phys Chem B (2014) 0.80
Multidrug resistance reversal effects of aminated thioxanthones and interaction with cytochrome P450 3A4. J Pharm Pharm Sci (2012) 0.80
Decomposing the energetic impact of drug-resistant mutations: the example of HIV-1 protease-DRV binding. Methods Mol Biol (2012) 0.80
Protein folding and binding: from biology to physics and back again. Curr Opin Struct Biol (2010) 0.78
Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases. Eur J Med Chem (2012) 0.78
Comparing ligand interactions with multiple receptors via serial docking. J Chem Inf Comput Sci (2004) 0.77
Enantioseparation and chiral recognition mechanism of new chiral derivatives of xanthones on macrocyclic antibiotic stationary phases. J Chromatogr A (2012) 0.77
Quantitative structure-activity relationship models with receptor-dependent descriptors for predicting peroxisome proliferator-activated receptor activities of thiazolidinedione and oxazolidinedione derivatives. Chem Biol Drug Des (2009) 0.76
Insight into the role of N,N-dimethylaminoethyl methacrylate (DMAEMA) conjugation onto poly(ethylenimine): cell viability and gene transfection studies. J Mater Sci Mater Med (2012) 0.76
The bioinformatics of molecular recognition. J Mol Recognit (2002) 0.76
Accelerated convergence of molecular free energy via superposition approximation-based reference states. J Chem Phys (2011) 0.76
Monoclonal antibodies raised against 167-180 aa sequence of human carbonic anhydrase XII inhibit its enzymatic activity. J Enzyme Inhib Med Chem (2014) 0.76
Charge Optimization Theory for Induced-Fit Ligands. J Chem Theory Comput (2012) 0.75
Comparative QSAR analyses of competitive CYP2C9 inhibitors using three-dimensional molecular descriptors. Chem Biol Drug Des (2011) 0.75
Discovery and characterization of novel selective inhibitors of carbonic anhydrase IX. J Med Chem (2014) 0.75
Interaction of antimicrobial peptides, BP100 and pepR, with model membrane systems as explored by Brownian dynamics simulations on a coarse-grained model. Biopolymers (2012) 0.75
Attractive interactions between heteroallenes and the cucurbituril portal. J Am Chem Soc (2017) 0.75
Molecular docking studies of the interaction between propargylic enol ethers and human DNA topoisomerase IIα. Bioorg Med Chem Lett (2013) 0.75
Interview with Celia Schiffer. Future Med Chem (2013) 0.75