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E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Assessing search strategies for flexible docking

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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation

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Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

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Development and testing of a general amber force field

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Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach

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Scalable molecular dynamics with NAMD

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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

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Respiratory syncytial virus inhibitors. Part 2: Benzimidazol-2-one derivatives

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Respiratory syncytial virus fusion inhibitors. Part 3: Water-soluble benzimidazol-2-one derivatives with antiviral activity in vivo

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Respiratory syncytial virus fusion inhibitors. Part 4: Optimization for oral bioavailability

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Respiratory syncytial virus fusion inhibitors. Part 5: Optimization of benzimidazole substitution patterns towards derivatives with improved activity

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Respiratory syncytial virus fusion inhibitors. Part 6: An examination of the effect of structural variation of the benzimidazol-2-one heterocycle moiety

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

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Discovery of LB30057, a benzamidrazone-based selective oral thrombin inhibitor

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Benzylamine-based selective and orally bioavailable inhibitors of thrombin

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Molecular recognition at the thrombin active site: structure-based design and synthesis of potent and selective thrombin inhibitors and the X-ray crystal structures of two thrombin-inhibitor complexes

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MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices

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Receptor Surface Models. 1. Definition and Construction

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Design, Synthesis, and Activity of a Novel Series of Factor Xa Inhibitors: Optimization of Arylamidine Groups

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Structure-Based de Novo Design, Synthesis, and Biological Evaluation of Non-Azole Inhibitors Specific for Lanosterol 14α-Demethylase of Fungi

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SDOCKER: A Method Utilizing Existing X-ray Structures To Improve Docking Accuracy

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Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring

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Design, Synthesis, and X-ray Structure of Potent Memapsin 2 (β-Secretase) Inhibitors with Isophthalamide Derivatives as the P2-P3-Ligands

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Structure-Guided Design of C2-Symmetric HIV-1 Protease Inhibitors Based on a Pyrrolidine Scaffold

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Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field

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Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

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Comparison of simple potential functions for simulating liquid water

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Structural characterization of the human respiratory syncytial virus fusion protein core

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Structure‐BasedDe NovoDrug Design

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3D‐e‐Chem: Structural Cheminformatics Workflows for Computer‐Aided Drug Discovery

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Exponential repulsion improves structural predictability of molecular docking

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Challenges and advances in computational docking: 2009 in review

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Fragment library design considerations

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Application of NMR and Molecular Docking in Structure-Based Drug Discovery

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Computational Approaches to Developing Short Cyclic Peptide Modulators of Protein–Protein Interactions

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Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein–Protein Interactions

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Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors

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De novo design by pharmacophore-based searches in fragment spaces

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Receptor–ligand molecular docking

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Mechanistic docking in terpene synthases using EnzyDock

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Synthesis and biological evaluation of modified pentapeptides as potent proteinase K inhibitors

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Structure-based optimization leads to the discovery of NSC765844, a highly potent, less toxic and orally efficacious dual PI3K/mTOR inhibitor

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Compound Collection Enhancement and Paradigms for High-Throughput Screening — an Update

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Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking

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Investigation of Crystal Structures in Structure-Based Virtual Screening for Protein Kinase Inhibitors

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CHARMM-GUI EnzyDocker for Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes

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EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes

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OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands

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Mechanisms of TPGS and its derivatives inhibiting P-glycoprotein efflux pump and application for reversing multidrug resistance in hepatocellular carcinoma

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Optimization of Benzoisothiazole dioxide inhibitory activity of the NS5B polymerase of HCV genotype 4 using ligand-steered homological modeling, reaction-driven scaffold-hopping and E-novo workflow

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