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CrystalDock: A Novel Approach to Fragment-Based Drug Design

https://doi.org/10.1021/ci200357y

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What this work says

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

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March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure

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Efficient Synthesis of Highly Active Phospha‐Isosteres of the Influenza Neuraminidase Inhibitor Oseltamivir

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Scalable molecular dynamics with NAMD

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

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Alchemical free energy simulations for biological complexes: powerful but temperamental …

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A Sialic Acid-derived Phosphonate Analog Inhibits Different Strains of Influenza Virus Neuraminidase with Different Efficiencies

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The Structures ofSalmonella typhimuriumLT2 Neuraminidase and its Complexes with Three Inhibitors at High Resolution

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Biphenyl amide p38 kinase inhibitors 1: Discovery and binding mode

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High Resolution Crystal Structure of a Key Editosome Enzyme from Trypanosoma brucei: RNA Editing Ligase 1

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Crystal Structure of the NanB Sialidase from Streptococcus pneumoniae

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HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis

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Alchemical free energy methods for drug discovery: progress and challenges

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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

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Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity

inferredcites →https://doi.org/10.1021/cr040426mopenalex-snapshot

Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

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Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies

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Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

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Synthesis of Tamiflu and its Phosphonate Congeners Possessing Potent Anti-Influenza Activity

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Discovery and Evaluation of 7-Alkyl-1,5-bis-aryl-pyrazolopyridinones as Highly Potent, Selective, and Orally Efficacious Inhibitors of p38α Mitogen-Activated Protein Kinase⊥⊥ Atomic coordinates and structure factors for crystal structure of compound3dwith p38α can be accessed using PDB code 3LHJ.

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Structural and Functional Basis of Resistance to Neuraminidase Inhibitors of Influenza B Viruses

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Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot

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

inferredcites →https://doi.org/10.1042/bj20060447openalex-snapshot

Structure-guided design of a novel class of benzyl-sulfonate inhibitors for influenza virus neuraminidase

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Comparison of simple potential functions for simulating liquid water

inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot

Amino acid substitution matrices from protein blocks.

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1107/s1744309109044935openalex-snapshot

Structure of D -lactate dehydrogenase fromAquifex aeolicuscomplexed with NAD+and lactic acid (or pyruvate)

inferredcites →https://doi.org/10.1128/jvi.00959-08openalex-snapshot

Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase

inferredcites →https://doi.org/10.1186/1741-7007-9-71openalex-snapshot

Molecular dynamics simulations and drug discovery

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Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1

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Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

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Treatment of Severe Cases of Pandemic (H1N1) 2009 Influenza: Review of Antivirals and Adjuvant Therapy

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Development of drug resistance in Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense. Treatment of human African trypanosomiasis with natural products (Review)

What points at this work

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

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Latest developments in molecular docking: 2010–2011 in review

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Identification of Similar Binding Sites to Detect Distant Polypharmacology

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The enumeration of chemical space

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Multiple Target Drug Design Using LigBuilder 3

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Designing Novel Inhibitors of Trypanosoma brucei

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A reverse combination of structure-based and ligand-based strategies for virtual screening

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CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities

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In silico fragment-based drug design with SEED

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BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation

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Subpocket Similarity-Based Hit Identification for Challenging Targets: Application to the WDR Domain of LRRK2

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A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design

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Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement

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Subpocket Analysis Method for Fragment-Based Drug Discovery

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SABRE: Ligand/Structure-Based Virtual Screening Approach Using Consensus Molecular-Shape Pattern Recognition

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POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics

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A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model

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Considerations of Protein Subpockets in Fragment‐Based Drug Design

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Fragment‐based drug discovery as alternative strategy to the drug development for neglected diseases

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Scoria: a Python module for manipulating 3D molecular data

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The Application of Fragment-based Approaches to the Discovery of Drugs for Neglected Tropical Diseases

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From Small to Powerful: The Fragments Universe and its “Chem-Appeal”

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Automatic Cavity Identification and Decomposition into Subpockets with CAVIAR

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Automatic Cavity Identification and Decomposition into Subpockets with CAVIAR

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LigBuilder V3: A Multi-Target de novo Drug Design Approach

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