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Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
inferredcites →https://doi.org/10.1002/1097-0134(20010201)42:2<256::aid-prot130>3.0.co;2-4openalex-snapshot
Efficient electrostatic solvation model for protein-fragment docking
inferredcites →https://doi.org/10.1002/cmdc.200900078openalex-snapshot
Discovery of Plasmepsin Inhibitors by Fragment‐Based Docking and Consensus Scoring
inferredcites →https://doi.org/10.1002/ijch.201300024openalex-snapshot
JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia
inferredcites →https://doi.org/10.1002/jcc.10306openalex-snapshot
Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
inferredcites →https://doi.org/10.1002/jcc.20035openalex-snapshot
Development and testing of a general amber force field
inferredcites →https://doi.org/10.1002/jcc.20065openalex-snapshot
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
inferredcites →https://doi.org/10.1002/jcc.21367openalex-snapshot
CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields
inferredcites →https://doi.org/10.1002/jcc.21797openalex-snapshot
Fast docking using the CHARMM force field with EADock DSS
inferredcites →https://doi.org/10.1002/jcc.21816openalex-snapshot
SwissParam: A fast force field generation tool for small organic molecules
inferredcites →https://doi.org/10.1002/jcc.21963openalex-snapshot
MATCH: An atom‐typing toolset for molecular mechanics force fields
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
inferredcites →https://doi.org/10.1002/prot.22028openalex-snapshot
Structure‐based tailoring of compound libraries for high‐throughput screening: Discovery of novel EphB4 kinase inhibitors
inferredcites →https://doi.org/10.1002/prot.340080302openalex-snapshot
Automated docking of substrates to proteins by simulated annealing
inferredcites →https://doi.org/10.1007/s00044-013-0571-yopenalex-snapshot
The discovery of potential cyclin A/CDK2 inhibitors: a combination of 3D QSAR pharmacophore modeling, virtual screening, and molecular docking studies
inferredcites →https://doi.org/10.1007/s10822-010-9395-8openalex-snapshot
Computer-aided drug design platform using PyMOL
inferredcites →https://doi.org/10.1007/s10822-013-9644-8openalex-snapshot
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/j.bmcl.2014.04.017openalex-snapshot
Discovery of BRD4 bromodomain inhibitors by fragment-based high-throughput docking
inferredcites →https://doi.org/10.1016/j.drudis.2014.03.004openalex-snapshot
Towards a sustainable system of drug development
inferredcites →https://doi.org/10.1016/j.jmgm.2005.12.005openalex-snapshot
Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1016/j.jmgm.2013.06.002openalex-snapshot
The emerging role of cloud computing in molecular modelling
inferredcites →https://doi.org/10.1016/j.jmgm.2013.10.004openalex-snapshot
Virtual screening of novel reversible inhibitors for marine alkaline protease MP
inferredcites →https://doi.org/10.1016/s1359-6446(04)03363-xopenalex-snapshot
The case for open-source software in drug discovery
inferredcites →https://doi.org/10.1016/s1359-6446(05)03692-5openalex-snapshot
Optimizing the use of open-source software applications in drug discovery
inferredcites →https://doi.org/10.1021/ci100474nopenalex-snapshot
Comparison of Computational Methods to Model DNA Minor Groove Binders
inferredcites →https://doi.org/10.1021/ci300363copenalex-snapshot
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
inferredcites →https://doi.org/10.1021/ci3003649openalex-snapshot
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
inferredcites →https://doi.org/10.1021/ci300399wopenalex-snapshot
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
inferredcites →https://doi.org/10.1021/ci800133bopenalex-snapshot
CHARMMing: A New, Flexible Web Portal for CHARMM
inferredcites →https://doi.org/10.1021/ci900056copenalex-snapshot
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
inferredcites →https://doi.org/10.1021/ct900079topenalex-snapshot
Validating CHARMM Parameters and Exploring Charge Distribution Rules in Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
inferredcites →https://doi.org/10.1021/jm049970dopenalex-snapshot
Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm060838iopenalex-snapshot
Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1021/ml3001984openalex-snapshot
Discovery of a Novel Chemotype of Tyrosine Kinase Inhibitors by Fragment-Based Docking and Molecular Dynamics
inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot
Virtual screening of chemical libraries
inferredcites →https://doi.org/10.1071/ch09463openalex-snapshot
Binding Mode Prediction of PDE4 Inhibitors: A Comparison of Modelling Methods
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1371/journal.pcbi.1003719openalex-snapshot
Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
inferredcites →https://doi.org/10.1371/journal.pcbi.1003738openalex-snapshot
Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding
inferredcites →https://doi.org/10.1371/journal.pcbi.1003739openalex-snapshot
Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins
inferredcites →https://doi.org/10.1515/bc.2001.168openalex-snapshot
Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
inferredcites →https://doi.org/10.1517/17460441.2013.794780openalex-snapshot
Automated docking for novel drug discovery
inferredcites →https://doi.org/10.3934/molsci.2014.2.81openalex-snapshot
Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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CIFDock : A novel CHARMM ‐based flexible receptor–flexible ligand docking protocol
inferred← citeshttps://doi.org/10.1002/minf.201501037openalex-snapshot
Software Infrastructure for Computer‐aided Drug Discovery and Development, a Practical Example with Guidelines
inferred← citeshttps://doi.org/10.1002/widm.1553openalex-snapshot
A brief review on quantum computing based drug design
inferred← citeshttps://doi.org/10.1007/7653_2015_51openalex-snapshot
Computational Fragment-Based Drug Design
inferred← citeshttps://doi.org/10.1007/s11030-022-10506-5openalex-snapshot
Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite
inferred← citeshttps://doi.org/10.1016/j.bpj.2019.11.3382openalex-snapshot
Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr
inferred← citeshttps://doi.org/10.1016/j.imr.2017.01.008openalex-snapshot
Quantitative analysis of multi-components by single marker—a rational method for the internal quality of Chinese herbal medicine
inferred← citeshttps://doi.org/10.1016/j.jcms.2015.05.006openalex-snapshot
Custom-made titanium devices as membranes for bone augmentation in implant treatment: Modeling accuracy of titanium products constructed with selective laser melting
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2015.02.006openalex-snapshot
In silico design of low molecular weight protein–protein interaction inhibitors: Overall concept and recent advances
inferred← citeshttps://doi.org/10.1016/j.semcancer.2021.07.012openalex-snapshot
Virtual screening of potential anticancer drugs based on microbial products
inferred← citeshttps://doi.org/10.1021/acs.chemrev.8b00630openalex-snapshot
Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00209openalex-snapshot
BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00534openalex-snapshot
ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00686openalex-snapshot
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00683openalex-snapshot
Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes
inferred← citeshttps://doi.org/10.1039/d1cp02001copenalex-snapshot
Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds
inferred← citeshttps://doi.org/10.1208/s12248-018-0216-7openalex-snapshot
Computational Fragment-Based Drug Design: Current Trends, Strategies, and Applications
inferred← citeshttps://doi.org/10.3390/ijms21114134openalex-snapshot
Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome
inferred← citeshttps://doi.org/10.3390/molecules24040681openalex-snapshot
The Good, the Bad, and the Ugly: “HiPen”, a New Dataset for Validating (S)QM/MM Free Energy Simulations
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch030openalex-snapshot
Molecular Docking at a Glance
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