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Reading PDB: 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/10.1002/jcc.540120716openalex-snapshot
Determination of molecular topology and atomic hybridization states from heavy atom coordinates
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/ci00062a008openalex-snapshot
SMILES. 2. Algorithm for generation of unique SMILES notation
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/ci200324eopenalex-snapshot
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats
inferredcites →https://doi.org/10.1021/ci700028wopenalex-snapshot
Automatic Perception of Organic Molecules Based on Essential Structural Information
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/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
inferredcites →https://doi.org/10.1093/bioinformatics/bth214openalex-snapshot
Ligand Depot: a data warehouse for ligands bound to macromolecules
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/ardp.202300661openalex-snapshot
SiteMine: Large‐scale binding site similarity searching in protein structure databases
inferred← citeshttps://doi.org/10.1002/jcc.24309openalex-snapshot
Automatic molecular structure perception for the universal force field
inferred← citeshttps://doi.org/10.1002/jcc.26522openalex-snapshot
LSLOpt : An open‐source implementation of the step‐length controlled LSL‐BFGS algorithm
inferred← citeshttps://doi.org/10.1007/s10822-024-00581-1openalex-snapshot
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.11.075openalex-snapshot
NAOMInext – Synthetically feasible fragment growing in a structure-based design context
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2017.06.004openalex-snapshot
From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library
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/10.1021/acs.jcim.0c01095openalex-snapshot
A Consistent Scheme for Gradient-Based Optimization of Protein – Ligand Poses
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00100openalex-snapshot
Modeling with Alternate Locations in X-ray Protein Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00336openalex-snapshot
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00292openalex-snapshot
MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing
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.5c03064openalex-snapshot
QuantumPDB: A Workflow for High-Throughput Quantum Cluster Model Generation from Protein Structures
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.6b00561openalex-snapshot
Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00150openalex-snapshot
Enabling Automatic Generation of Protein–Ligand Complex Data Sets with Atomistic Detail
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00291openalex-snapshot
NAOMI nova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00757openalex-snapshot
Conservation and Relevance of Pharmacophore Point Types
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/10.1021/acs.jmedchem.6c00089openalex-snapshot
Predicting Ligand Binding Modes by Scaffold-Guided Structure Refinement
inferred← citeshttps://doi.org/10.1021/ci500131xopenalex-snapshot
Benchmark Data Sets for Structure-Based Computational Target Prediction
inferred← citeshttps://doi.org/10.1093/bib/bbad357openalex-snapshot
Searching similar local 3D micro-environments in protein structure databases with MicroMiner
inferred← citeshttps://doi.org/10.1107/s1600576726005625openalex-snapshot
Rep3D : an algorithm to identify structurally similar motifs
inferred← citeshttps://doi.org/10.1107/s205979832300582xopenalex-snapshot
LifeSoaks : a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments
inferred← citeshttps://doi.org/10.1145/3583780.3614974openalex-snapshot
MPerformer: An SE(3) Transformer-based Molecular Perceptron
inferred← citeshttps://doi.org/10.1186/1758-2946-5-38openalex-snapshot
MONA – Interactive manipulation of molecule collections
inferred← citeshttps://doi.org/10.1186/1758-2946-6-12openalex-snapshot
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
inferred← citeshttps://doi.org/10.1186/s13321-018-0293-8openalex-snapshot
PubChem chemical structure standardization
inferred← citeshttps://doi.org/10.1186/s13321-019-0340-0openalex-snapshot
Automated simultaneous assignment of bond orders and formal charges
inferred← citeshttps://doi.org/10.2174/0929867326666190614160451openalex-snapshot
VSPrep: A KNIME Workflow for the Preparation of Molecular Databases for Virtual Screening
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.7813130openalex-snapshot
Additional file 1 of Automated simultaneous assignment of bond orders and formal charges
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