A geometric approach to macromolecule-ligand interactions.

PubWeight™: 5.71‹?› | Rank: Top 1%

🔗 View Article (PMID 7154081)

Published in J Mol Biol on October 25, 1982

Authors

I D Kuntz, J M Blaney, S J Oatley, R Langridge, T E Ferrin

Articles citing this

(truncated to the top 100)

PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66

Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci (1998) 7.03

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A (1992) 6.86

Benchmarking sets for molecular docking. J Med Chem (2006) 5.57

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des (2001) 4.54

Protein clefts in molecular recognition and function. Protein Sci (1996) 4.20

Comparative study of several algorithms for flexible ligand docking. J Comput Aided Mol Des (2003) 3.29

A review of protein-small molecule docking methods. J Comput Aided Mol Des (2002) 3.25

A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010) 3.05

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des (2013) 2.93

Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des (2000) 2.84

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (2009) 2.83

A role for surface hydrophobicity in protein-protein recognition. Protein Sci (1994) 2.59

Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des (2006) 2.50

Structure-based discovery of beta2-adrenergic receptor ligands. Proc Natl Acad Sci U S A (2009) 2.48

Flexible ligand docking using conformational ensembles. Protein Sci (1998) 2.43

TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res (2006) 2.26

Automated docking screens: a feasibility study. J Med Chem (2009) 2.14

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol (2008) 2.03

Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des (2001) 1.97

Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem (2005) 1.79

Target flexibility: an emerging consideration in drug discovery and design. J Med Chem (2008) 1.74

Structure-based discovery of A2A adenosine receptor ligands. J Med Chem (2010) 1.71

Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des (2002) 1.68

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J Chem Inf Model (2011) 1.61

Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci (2002) 1.61

Advances and challenges in protein-ligand docking. Int J Mol Sci (2010) 1.54

Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des (2011) 1.53

Computational methods in drug discovery. Pharmacol Rev (2013) 1.51

Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci U S A (2000) 1.50

Rational design and characterization of platelet factor 4 antagonists for the study of heparin-induced thrombocytopenia. Blood (2012) 1.50

Soft docking and multiple receptor conformations in virtual screening. J Med Chem (2004) 1.47

Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci U S A (1990) 1.46

Decoys for docking. J Med Chem (2005) 1.43

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

MedusaScore: an accurate force field-based scoring function for virtual drug screening. J Chem Inf Model (2008) 1.37

Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res (2008) 1.36

Molecular docking screens using comparative models of proteins. J Chem Inf Model (2009) 1.36

Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Sci (2009) 1.35

Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des (2000) 1.35

Discovery and characterization of a small molecule inhibitor of the PDZ domain of dishevelled. J Biol Chem (2009) 1.34

HotPatch: a statistical approach to finding biologically relevant features on protein surfaces. J Mol Biol (2007) 1.32

Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des (2012) 1.27

Pleiotropic mechanisms facilitated by resveratrol and its metabolites. Biochem J (2010) 1.26

Docking validation resources: protein family and ligand flexibility experiments. J Chem Inf Model (2010) 1.25

Evaluation of DOCK 6 as a pose generation and database enrichment tool. J Comput Aided Mol Des (2012) 1.22

Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des (2007) 1.21

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci (2005) 1.20

Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J Chem Inf Model (2009) 1.19

Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome. PLoS Comput Biol (2009) 1.18

Probing molecular docking in a charged model binding site. J Mol Biol (2006) 1.17

A small molecule agonist of EphA2 receptor tyrosine kinase inhibits tumor cell migration in vitro and prostate cancer metastasis in vivo. PLoS One (2012) 1.15

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des (2009) 1.11

Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay. J Med Chem (2008) 1.11

Customizing scoring functions for docking. J Comput Aided Mol Des (2008) 1.11

Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem (2008) 1.10

DOCK 6: Impact of new features and current docking performance. J Comput Chem (2015) 1.07

MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics (2008) 1.07

Targeting fatty acid binding protein (FABP) anandamide transporters - a novel strategy for development of anti-inflammatory and anti-nociceptive drugs. PLoS One (2012) 1.07

The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des (1999) 1.06

Can we separate active from inactive conformations? J Comput Aided Mol Des (2002) 1.06

Novel human mPGES-1 inhibitors identified through structure-based virtual screening. Bioorg Med Chem (2011) 1.05

Computational drug discovery. Acta Pharmacol Sin (2012) 1.04

Optimal assignment methods for ligand-based virtual screening. J Cheminform (2009) 1.03

Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des (1997) 1.02

Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons. J Comput Chem (2011) 1.02

McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm. J Mol Model (2009) 1.02

Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro. Biochem J (1996) 1.02

Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD. Chem Biol (2009) 1.01

AutoGrow: a novel algorithm for protein inhibitor design. Chem Biol Drug Des (2009) 1.01

A novel and efficient tool for locating and characterizing protein cavities and binding sites. Proteins (2010) 1.01

Accessible high-throughput virtual screening molecular docking software for students and educators. PLoS Comput Biol (2012) 1.01

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J (2010) 0.99

Computational methods of studying the binding of toxins from venomous animals to biological ion channels: theory and applications. Physiol Rev (2013) 0.99

Small-molecule Bax agonists for cancer therapy. Nat Commun (2014) 0.99

Ligand pose and orientational sampling in molecular docking. PLoS One (2013) 0.99

Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med (2009) 0.98

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des (2013) 0.97

Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys J (2003) 0.96

Discovery of a novel selective kappa-opioid receptor agonist using crystal structure-based virtual screening. J Chem Inf Model (2013) 0.96

Molecular modeling of the reductase domain to elucidate the reaction mechanism of reduction of peptidyl thioester into its corresponding alcohol in non-ribosomal peptide synthetases. BMC Struct Biol (2010) 0.96

Filtering databases and chemical libraries. J Comput Aided Mol Des (2002) 0.96

Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J Comput Chem (2012) 0.96

Identification of novel target sites and an inhibitor of the dengue virus E protein. J Comput Aided Mol Des (2009) 0.96

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Res (2014) 0.95

Design of a grid service-based platform for in silico protein-ligand screenings. Comput Methods Programs Biomed (2008) 0.95

Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure. Bioorg Med Chem Lett (2006) 0.95

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J Med Chem (2005) 0.95

Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen (2005) 0.94

Inhibition of pyrimidine synthesis reverses viral virulence factor-mediated block of mRNA nuclear export. J Cell Biol (2012) 0.94

High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. J Biol Chem (2012) 0.94

F2Dock: fast Fourier protein-protein docking. IEEE/ACM Trans Comput Biol Bioinform (2010) 0.94

Ligand binding mode prediction by docking: mdm2/mdmx inhibitors as a case study. J Chem Inf Model (2014) 0.93

An inverse docking approach for identifying new potential anti-cancer targets. J Mol Graph Model (2011) 0.92

Test of the Binding Threshold Hypothesis for olfactory receptors: explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912-93. Protein Sci (2005) 0.92

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor. J Comput Aided Mol Des (2002) 0.91

Using RosettaLigand for small molecule docking into comparative models. PLoS One (2012) 0.90

Strategies for the determination of pharmacophoric 3D database queries. J Comput Aided Mol Des (1997) 0.90

A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data. Protein Sci (2001) 0.89

Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. Biophys J (2004) 0.89

Articles by these authors

Hydration of proteins and polypeptides. Adv Protein Chem (1974) 6.25

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des (2001) 4.54

Structure of prealbumin: secondary, tertiary and quaternary interactions determined by Fourier refinement at 1.8 A. J Mol Biol (1978) 4.47

Improvements in protein secondary structure prediction by an enhanced neural network. J Mol Biol (1990) 4.10

Crystallographic studies of the dynamic properties of lysozyme. Nature (1979) 3.30

Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A. Biochemistry (1984) 3.05

High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc Natl Acad Sci U S A (2000) 2.96

Hydration of macromolecules. Science (1969) 2.88

The properties of water in biological systems. Annu Rev Biophys Bioeng (1974) 2.62

Optical diffraction studies of muscle fibers. Biophys J (1973) 2.40

Hydration of macromolecules. IV. Polypeptide conformation in frozen solutions. J Am Chem Soc (1971) 2.34

Molecular cloning and nucleotide sequence of the streptavidin gene. Nucleic Acids Res (1986) 2.30

Thermal expansion of a protein. Biochemistry (1987) 2.25

Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J Med Chem (1988) 2.20

Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science (1987) 2.04

Physical and enzymatic studies on poly d(I-C)-poly d(I-C), an unusual double-helical DNA. Nature (1970) 2.04

Protein folding. J Am Chem Soc (1972) 1.98

Free energy calculations by computer simulation. Science (1987) 1.98

Protein docking and complementarity. J Mol Biol (1991) 1.86

Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci U S A (1993) 1.82

Molecular docking to ensembles of protein structures. J Mol Biol (1997) 1.80

Crystal structures of Escherichia coli dihydrofolate reductase: the NADP+ holoenzyme and the folate.NADP+ ternary complex. Substrate binding and a model for the transition state. Biochemistry (1990) 1.71

Mutational and secondary structural analysis of the basolateral sorting signal of the polymeric immunoglobulin receptor. J Cell Biol (1993) 1.68

Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis. Science (1986) 1.68

Ligand solvation in molecular docking. Proteins (1999) 1.65

Turn prediction in proteins using a pattern-matching approach. Biochemistry (1986) 1.65

Structure-based discovery of inhibitors of thymidylate synthase. Science (1993) 1.61

The structure of a DNA-RNA hybrid. Proc Natl Acad Sci U S A (1967) 1.61

Matching chemistry and shape in molecular docking. Protein Eng (1993) 1.53

Electrostatic potential molecular surfaces. Proc Natl Acad Sci U S A (1982) 1.53

Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones. Biochemistry (1993) 1.51

Protein-DNA and protein-hormone interactions in prealbumin: a model of the thyroid hormone nuclear receptor? Nature (1977) 1.51

Taxonomy and conformational analysis of loops in proteins. J Mol Biol (1992) 1.48

Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol (1996) 1.48

A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers (1991) 1.47

Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proc Natl Acad Sci U S A (1990) 1.46

Conic: a fast renderer for space-filling molecules with shadows. J Mol Graph (1991) 1.40

X-ray fiber diffraction evidence for neighbor exclusion binding of a platinum metallointercalation reagent to DNA. Proc Natl Acad Sci U S A (1975) 1.39

Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance. J Mol Biol (1990) 1.38

Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. Chem Biol (1997) 1.35

Measuring diversity: experimental design of combinatorial libraries for drug discovery. J Med Chem (1995) 1.33

Nuclear magnetic resonance studies of xenon-129 with myoglobin and hemoglobin. Biochemistry (1982) 1.32

Real-time color graphics in studies of molecular interactions. Science (1981) 1.31

X-ray diffraction studies of double helical ribonucleic acid. Nature (1966) 1.31

Crystal structure of Escherichia coli thymidylate synthase containing bound 5-fluoro-2'-deoxyuridylate and 10-propargyl-5,8-dideazafolate. J Mol Biol (1990) 1.31

Crystal structure of a novel trimethoprim-resistant dihydrofolate reductase specified in Escherichia coli by R-plasmid R67. Biochemistry (1986) 1.29

Mutants of bovine pancreatic trypsin inhibitor lacking cysteines 14 and 38 can fold properly. Science (1987) 1.29

Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity. J Virol (1997) 1.29

Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des (1995) 1.27

Calculation of protein tertiary structure. J Mol Biol (1976) 1.27

Tertiary structure in carboxypeptidase. J Am Chem Soc (1972) 1.25

An engineered disulfide bond in dihydrofolate reductase. Biochemistry (1987) 1.20

Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science (1983) 1.19

The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. J Theor Biol (1983) 1.19

A new approach to the problem of docking two molecules: the ellipsoid algorithm. Biopolymers (1987) 1.18

Structurally specific binding of halogenated biphenyls to thyroxine transport protein. J Med Chem (1986) 1.17

Distance measurements in spin-labeled lysozyme. Biochemistry (1984) 1.16

Molecular and crystal structures of double-helical RNA. 3. An 11-fold molecular model and comparison of the agreement between the observed and calculated three-dimensional diffraction data for 10- and 11-fold models. J Mol Biol (1967) 1.14

Molecular dynamics simulations of small peptides: dependence on dielectric model and pH. Biopolymers (1991) 1.14

Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther (2011) 1.14

Structure-based design of parasitic protease inhibitors. Bioorg Med Chem (1996) 1.12

An approach to the tertiary structure of globular proteins. J Am Chem Soc (1975) 1.11

Molecular docking towards drug discovery. J Mol Recognit (1997) 1.10

X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis. Biochemistry (1990) 1.10

Conformation spaces of proteins. Proteins (2001) 1.09

Protein densities. Int J Pept Protein Res (1979) 1.09

Secondary structure assignment for alpha/beta proteins by a combinatorial approach. Biochemistry (1983) 1.08

Computational studies of the interaction of myoglobin and xenon. J Mol Biol (1986) 1.08

Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proc Natl Acad Sci U S A (1996) 1.07

Leishmania major: molecular modeling of cysteine proteases and prediction of new nonpeptide inhibitors. Exp Parasitol (1997) 1.07

Molecular interactions of toxic chlorinated dibenzo-p-dioxins and dibenzofurans with thyroxine binding prealbumin. J Med Chem (1985) 1.07

Molecular modeling software and methods for medicinal chemistry. J Med Chem (1990) 1.07

A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clin Pharmacol Ther (2011) 1.07

Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. J Comput Aided Mol Des (1996) 1.02

Structure of guanylyl-3',5'-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2(1). Biopolymers (1975) 1.02

Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro. Biochem J (1996) 1.02

Protein-ligand dynamics. A 96 picosecond simulation of a myoglobin-xenon complex. J Mol Biol (1988) 1.02

Two-dimensional 1H NMR of three spin-labeled derivatives of bovine pancreatic trypsin inhibitor. Biochemistry (1986) 1.01

Conformational analysis using distance geometry methods. J Mol Graph Model (1997) 1.01

Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II. J Med Chem (1999) 1.01

Diffusion-collision model for the folding kinetics of myoglobin. Proteins (1988) 1.01

CHORTLES: a method for representing oligomeric and template-based mixtures. J Chem Inf Comput Sci (1996) 1.00

Conformational switching in designed peptides: the helix/sheet transition. Fold Des (1996) 1.00

Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations. Biopolymers (1975) 1.00

Nature of steroid-glucocorticoid receptor interactions: thermodynamic analysis of the binding reaction. Biochemistry (1978) 1.00

Structure-activity studies of interleukin-2. Science (1986) 1.00

Hydration of macromolecules. II. Effects of urea on protein hydration. Arch Biochem Biophys (1971) 1.00

Adenosine analogues as selective inhibitors of glyceraldehyde-3-phosphate dehydrogenase of Trypanosomatidae via structure-based drug design. J Med Chem (2001) 1.00

Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors. J Comput Aided Mol Des (1995) 1.00

CHUCKLES: a method for representing and searching peptide and peptoid sequences on both monomer and atomic levels. J Chem Inf Comput Sci (1994) 0.99

Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry (1999) 0.98

NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library. Mol Divers (1997) 0.98

Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. J Biol Chem (1993) 0.98

Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation. Proc Natl Acad Sci U S A (1996) 0.97

Flexible ligand docking: a multistep strategy approach. Proteins (1999) 0.97