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On the Perception of Molecules from 3D Atomic Coordinates
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1021/ci00002a004openalex-snapshot
The development of versions 3 and 4 of the Cambridge Structural Database System
inferredcites →https://doi.org/10.1021/ci00009a001openalex-snapshot
Automatic assignment of chemical connectivity to organic molecules in the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci00016a013openalex-snapshot
Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci9603487openalex-snapshot
BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank
inferredcites →https://doi.org/10.1107/s0907444998007124openalex-snapshot
Databases for Protein–Ligand Complexes
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527840748.ch7openalex-snapshot
Recent Advances in Practical Quantum Mechanics and M ixed‐QM / MM ‐Driven X‐Ray Crystallography and Cryogenic Electron Microscopy ( Cryo‐EM ) and Their Impact on Structure‐Based Drug Discovery
inferred← citeshttps://doi.org/10.1002/bkcs.10334openalex-snapshot
Universal Structure Conversion Method for Organic Molecules: From Atomic Connectivity to Three‐Dimensional Geometry
inferred← citeshttps://doi.org/10.1002/chin.200522213openalex-snapshot
Perception of Molecules from 3D Atomic Coordinates.
inferred← citeshttps://doi.org/10.1002/jcc.24309openalex-snapshot
Automatic molecular structure perception for the universal force field
inferred← citeshttps://doi.org/10.1007/978-3-032-29730-3_13openalex-snapshot
Benchmark First: Defining Tasks for Graph Transformation Learning
inferred← citeshttps://doi.org/10.1007/s10822-010-9329-5openalex-snapshot
So you think you understand tautomerism?
inferred← citeshttps://doi.org/10.1016/j.actbio.2017.01.049openalex-snapshot
A photoresponsive soft interface reversibly controls wettability and cell adhesion by conformational changes in a spiropyran-conjugated amphiphilic block copolymer
inferred← citeshttps://doi.org/10.1016/j.comptc.2019.112508openalex-snapshot
The dataset of covalent bond lengths resulting from the first-principle calculations
inferred← citeshttps://doi.org/10.1016/j.febslet.2006.02.003openalex-snapshot
A complete small molecule dataset from the protein data bank
inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.07.002openalex-snapshot
Reaction analysis and visualization of ReaxFF molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.08.023openalex-snapshot
IM-UFF: Extending the universal force field for interactive molecular modeling
inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.10.010openalex-snapshot
A fast approximate algorithm for determining bond orders in large polycyclic structures
inferred← citeshttps://doi.org/10.1016/j.tcs.2010.12.063openalex-snapshot
Computing bond orders in molecule graphs
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00512openalex-snapshot
Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c03052openalex-snapshot
Multimodal Bond Reconstruction toward Generative Molecular Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00069openalex-snapshot
UNICON: A Powerful and Easy-to-Use Compound Library Converter
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00151openalex-snapshot
Reliable and Performant Identification of Low-Energy Conformers in the Gas Phase and Water
inferred← citeshttps://doi.org/10.1021/acsinfecdis.6b00113openalex-snapshot
A Comprehensive Computational Analysis for the Binding Modes of Hepatitis C Virus NS5A Inhibitors: The Question of Symmetry
inferred← citeshttps://doi.org/10.1021/ci049645zopenalex-snapshot
Correct Bond Order Assignment in a Molecular Framework Using Integer Linear Programming with Application to Molecules Where Only Non-Hydrogen Atom Coordinates Are Available
inferred← citeshttps://doi.org/10.1021/ci050372xopenalex-snapshot
sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank
inferred← citeshttps://doi.org/10.1021/ci050400bopenalex-snapshot
The Blue Obelisk—Interoperability in Chemical Informatics
inferred← citeshttps://doi.org/10.1021/ci300358copenalex-snapshot
Reading PDB: Perception of Molecules from 3D Atomic Coordinates
inferred← citeshttps://doi.org/10.1021/ci700028wopenalex-snapshot
Automatic Perception of Organic Molecules Based on Essential Structural Information
inferred← citeshttps://doi.org/10.1063/5.0016011openalex-snapshot
Bond order predictions using deep neural networks
inferred← citeshttps://doi.org/10.1088/1674-1056/27/2/020503openalex-snapshot
Optimizing the atom types of proteins through iterative knowledge-based potentials
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq718openalex-snapshot
Automated bond order assignment as an optimization problem
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr055openalex-snapshot
fconv: format conversion, manipulation and feature computation of molecular data
inferred← citeshttps://doi.org/10.1107/s0108768111024608openalex-snapshot
Deducing chemical structure from crystallographically determined atomic coordinates
inferred← citeshttps://doi.org/10.1107/s1399004714002260openalex-snapshot
Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics programDivConinto thePHENIXrefinement package
inferred← citeshttps://doi.org/10.1124/dmd.112.045583openalex-snapshot
Potent Inhibition of Human Sulfotransferase 1A1 by 17α-Ethinylestradiol: Role of 3′-Phosphoadenosine 5′-Phosphosulfate Binding and Structural Rearrangements in Regulating Inhibition and Activity
inferred← citeshttps://doi.org/10.1145/3583780.3614974openalex-snapshot
MPerformer: An SE(3) Transformer-based Molecular Perceptron
inferred← citeshttps://doi.org/10.1186/1471-2105-7-152openalex-snapshot
Domain-based small molecule binding site annotation
inferred← citeshttps://doi.org/10.1186/1758-2946-4-26openalex-snapshot
A rule-based algorithm for automatic bond type perception
inferred← citeshttps://doi.org/10.1186/s13321-019-0340-0openalex-snapshot
Automated simultaneous assignment of bond orders and formal charges
inferred← citeshttps://doi.org/10.1186/s13321-023-00780-2openalex-snapshot
A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
inferred← citeshttps://doi.org/10.1371/journal.pone.0118290openalex-snapshot
Discovery of Novel New Delhi Metallo-β-Lactamases-1 Inhibitors by Multistep Virtual Screening
inferred← citeshttps://doi.org/10.1515/hmbci.2010.012openalex-snapshot
Structural rearrangement of SULT2A1: effects on dehydroepiandrosterone and raloxifene sulfation
inferred← citeshttps://doi.org/10.26434/chemrxiv.7403630.v2openalex-snapshot
Perception of Chemical Bonds via Machine Learning
inferred← citeshttps://doi.org/10.6084/m9.figshare.26656354openalex-snapshot
Additional file 1 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
inferred← citeshttps://doi.org/10.6084/m9.figshare.26656357openalex-snapshot
Additional file 2 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
inferred← citeshttps://doi.org/10.6084/m9.figshare.26656360openalex-snapshot
Additional file 3 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
inferred← citeshttps://doi.org/10.6084/m9.figshare.26656363openalex-snapshot
Additional file 4 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
inferred← citeshttps://doi.org/10.6084/m9.figshare.7813130openalex-snapshot
Additional file 1 of Automated simultaneous assignment of bond orders and formal charges
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