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Receptor Flexibility in de Novo Ligand Design and Docking
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Docking small ligands in flexible binding sites
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Flexible protein–ligand docking by global energy optimization in internal coordinates
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Side-chain flexibility in proteins upon ligand binding
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Computer simulations of ligand-protein binding with ensembles of protein conformations: A Monte Carlo study of HIV-1 protease binding energy landscapes
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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Bayesian statistical analysis of protein side‐chain rotamer preferences
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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Backbone-dependent Rotamer Library for Proteins Application to Side-chain Prediction
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool
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Side-chain and backbone flexibility in protein core design 1 1Edited by A. R. Fersht
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Automatic protein design with all atom force-fields by exact and heuristic optimization 1 1Edited by J. Thorton
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Extending the accuracy limits of prediction for side-chain conformations
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The computer program LUDI: A new method for the de novo design of enzyme inhibitors
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SPROUT: A program for structure generation
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Inhibitory effect of pyruvate on release of glutathione and swelling of rat heart mitochondria
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The role of matrix metalloproteinases in heart disease
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Ligand-Induced Conformational Changes: Improved Predictions of Ligand Binding Conformations and Affinities
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Efficient Conformational Sampling of Local Side-chain Flexibility
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Ligand docking to proteins with discrete side-chain flexibility
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Accommodating Protein Flexibility in Computational Drug Design,
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Substituted piperidines - highly potent renin inhibitors due to induced fit adaptation of the active site
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Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere
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Structure of acetylcholinesterase complexed with E2020 (Aricept®): implications for the design of new anti-Alzheimer drugs
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A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening
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NMR Solution Structure of the Catalytic Fragment of Human Fibroblast Collagenase Complexed with a Sulfonamide Derivative of a Hydroxamic Acid Compound
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Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
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Comparing Ligand Interactions with Multiple Receptors via Serial Docking
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RECAPRetrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry
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Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
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Detailed Analysis of Scoring Functions for Virtual Screening
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Designing Non-Peptide Peptidomimetics in the 21st Century: Inhibitors Targeting Conformational Ensembles
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Multiple Active Site Corrections for Docking and Virtual Screening
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Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
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Receptor Flexibility in the in Silico Screening of Reagents in the S1‘ Pocket of Human Collagenase
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HIV-Reverse Transcriptase Inhibition: Inclusion of Ligand-Induced Fit by Cross-Docking Studies
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Raptor: Combining Dual-Shell Representation, Induced-Fit Simulation, and Hydrophobicity Scoring in Receptor Modeling: Application toward the Simulation of Structurally Diverse Ligand Sets
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Assessment of Multiple Binding Modes in Ligand−Protein Docking
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Matrix metalloproteinase inhibitors
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The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
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Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
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Virtual screening with solvation and ligand-induced complementarity
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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Structure-based ligand design for flexible proteins: Application of new F-DycoBlock
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A validation study on the practical use of automated de novo design
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Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint
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The dead-end elimination theorem and its use in protein side-chain positioning
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Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors.
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Implications of protein flexibility for drug discovery
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Structure of acetylcholinesterase complexed with the nootropic alkaloid, (–)-huperzine A
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Structure of the catalytic domain of human fibroblast collagenase complexed with an inhibitor
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Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancerdrug 1843U89
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Computational ligand design by free energy minimization
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Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces
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Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.
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The fuzzy-end elimination theorem: correctly implementing the side chain placement algorithm based on the dead-end elimination theorem
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Finding the global minimum: a fuzzy end elimination implementation
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Three‐dimensional structures of Drosophila melanogaster acetylcholinesterase and of its complexes with two potent inhibitors
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A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics
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Matrix Metalloproteinase Inhibitors and Cancer—Trials and Tribulations
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Drug Delivery Systems: Entering the Mainstream
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The Many Roles of Computation in Drug Discovery
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De Novo Protein Design: Fully Automated Sequence Selection
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Matrix metalloproteinase inhibitors 1998
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Protein Flexibility is an Important Component of Structure-Based Drug Discovery
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Docking and Scoring in Drug Discovery
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HIV‐1 NNRTIs: structural diversity, pharmacophore similarity, and impliations for drug design
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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
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Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model
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Protein flexibility in docking and surface mapping
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Protein Flexibility in Docking-Based Virtual Screening: Discovery of Novel Lymphoid-Specific Tyrosine Phosphatase Inhibitors Using Multiple Crystal Structures
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