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BALI: Automatic Assignment of Bond and Atom Types for Protein Ligands in the Brookhaven Protein Databank

https://doi.org/10.1021/ci9603487
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What this work says

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

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Pseudooxokohlenstoff‐Dianionen der C4‐Reihe mit Dicyanmethylenfunktionen
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The protein data bank: A computer-based archival file for macromolecular structures
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The development of versions 3 and 4 of the Cambridge Structural Database System
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Chemical Abstracts Service Chemical Registry System. 13. Enhanced handling of stereochemistry
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Automatic assignment of chemical connectivity to organic molecules in the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci00057a005openalex-snapshot
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
inferredcites →https://doi.org/10.1021/ja00435a040openalex-snapshot
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Ultraviolet and .gamma.-ray-induced free-radical reactions of nucleic acid constituents. Selectivity of some reactions for purines. Suppression of the reactivity of pyrimidines
inferredcites →https://doi.org/10.1039/c39770000790openalex-snapshot
Reaction of tetracycline hydrochloride with N-chlorosuccinimide: X-ray crystal structure of the major product

What points at this work

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

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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
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A complete small molecule dataset from the protein data bank
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Reaction analysis and visualization of ReaxFF molecular dynamics simulations
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Computing bond orders in molecule graphs
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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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Correct Bond Order Assignment in a Molecular Framework Using Integer Linear Programming with Application to Molecules Where Only Non-Hydrogen Atom Coordinates Are Available
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Retrieval of Crystallographically-Derived Molecular Geometry Information
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LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters
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On the Perception of Molecules from 3D Atomic Coordinates
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Reading PDB: Perception of Molecules from 3D Atomic Coordinates
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Automatic Perception of Organic Molecules Based on Essential Structural Information
inferred← citeshttps://doi.org/10.1021/ci9904214openalex-snapshot
SATIS: Atom Typing from Chemical Connectivity
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PDBLIG: Classification of Small Molecular Protein Binding in the Protein Data Bank
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Investigation of asymmetric alcohol dehydrogenase (ADH) reduction of acetophenone derivatives: effect of charge density
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Bond order predictions using deep neural networks
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Automated bond order assignment as an optimization problem
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fconv: format conversion, manipulation and feature computation of molecular data
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Remediation of the protein data bank archive
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Deducing chemical structure from crystallographically determined atomic coordinates
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MPerformer: An SE(3) Transformer-based Molecular Perceptron
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Virtual screening and evaluation of Ketol-Acid Reducto-Isomerase (KARI) as a putative drug target for Aspergillosis
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A rule-based algorithm for automatic bond type perception
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PubChem chemical structure standardization
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Automated simultaneous assignment of bond orders and formal charges
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A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Perception of Chemical Bonds via Machine Learning
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Additional file 1 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Additional file 2 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Additional file 3 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Additional file 4 of A workflow for deriving chemical entities from crystallographic data and its application to the Crystallography Open Database
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Additional file 1 of Automated simultaneous assignment of bond orders and formal charges
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