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Automatic Perception of Organic Molecules Based on Essential Structural Information

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What this work says

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

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Ring Perception: Proof of a Formula Calculating the Number of the Smallest Rings in Connected Graphs
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/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
inferredcites →https://doi.org/10.1021/ci049915dopenalex-snapshot
On the Perception of Molecules from 3D Atomic Coordinates
inferredcites →https://doi.org/10.1021/ci9603487openalex-snapshot
BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank

What points at this work

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

inferred← citeshttps://doi.org/10.1002/chin.200740207openalex-snapshot
Automatic Perception of Organic Molecules Based on Essential Structural Information.
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Predicting Molecular Targets for Small‐Molecule Drugs with a Ligand‐Based Interaction Fingerprint Approach
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Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes
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Automatic molecular structure perception for the universal force field
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Multiple Target Drug Design Using LigBuilder 3
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Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses
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A systematical comparison of DFT methods in reproducing the interaction energies of halide series with protein moieties
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Structure-based grafting and identification of kinase–inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma
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Use of QM/MM scheme to reproduce macromolecule–small molecule noncovalent binding energy
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Strain energy in enzyme–substrate binding: An energetic insight into the flexibility versus rigidity of enzyme active site
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Complexation of trans- and cis-resveratrol with bovine serum albumin, β-lactoglobulin or α-lactalbumin
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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
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Formation of a Multiligand Complex of Bovine Serum Albumin with Retinol, Resveratrol, and (−)-Epigallocatechin-3-gallate for the Protection of Bioactive Components
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00076openalex-snapshot
Molecular Perception for Visualization and Computation: The Proxima Library
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.6b00069openalex-snapshot
UNICON: A Powerful and Easy-to-Use Compound Library Converter
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00545openalex-snapshot
Comparative Assessment of Scoring Functions: The CASF-2016 Update
inferred← citeshttps://doi.org/10.1021/ci300358copenalex-snapshot
Reading PDB: Perception of Molecules from 3D Atomic Coordinates
inferred← citeshttps://doi.org/10.1021/ci500080qopenalex-snapshot
Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
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Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results
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Comparative Assessment of Scoring Functions on a Diverse Test Set
inferred← citeshttps://doi.org/10.1021/ct100167wopenalex-snapshot
Halogen-Ionic Bridges: Do They Exist in the Biomolecular World?
inferred← citeshttps://doi.org/10.1021/ct800267xopenalex-snapshot
Geometrical Preferences of the Hydrogen Bonds on Protein−Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
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
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Computational Analysis and Molecular Design of Aromatic Stacking System Between Human ARTD2 Catalytic Domain and its Small-Molecule Inhibitors and Peptidic Ligands
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Integrated Establishment of Human VEGFR2 V916M Gatekeeper Mutation and Rational Discovery of Staralogs as Wild Type–Sparing, V916M–Selective Inhibitors Using Analog–Sensitive Kinase Technology
inferred← citeshttps://doi.org/10.1145/3583780.3614974openalex-snapshot
MPerformer: An SE(3) Transformer-based Molecular Perceptron
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A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction
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/10.26434/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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