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Comprehensive Classification and Diversity Assessment of Atomic Contacts in Protein–Small Ligand Interactions

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What this work says

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

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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Validation of the general purpose tripos 5.2 force field

inferredcites →https://doi.org/10.1002/prot.21253openalex-snapshot

Strong and weak hydrogen bonds in the protein–ligand interface

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X-SITE: Use of Empirically Derived Atomic Packing Preferences to Identify Favourable Interaction Regions in the Binding Sites of Proteins

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SuperStar: A Knowledge-based Approach for Identifying Interaction Sites in Proteins

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Superstar: improved knowledge-based interaction fields for protein binding sites11Edited by R. Huber

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Superstar: comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions 1 1Edited by R. Huber

inferredcites →https://doi.org/10.1006/jmbi.2001.5023openalex-snapshot

A fragment library based on gaussian mixtures predicting favorable molecular interactions 1 aEdited by G. von Heijne

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The success of structural genomics

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Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era

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Structure-based drug design to augment hit discovery

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PSI-2: Structural Genomics to Cover Protein Domain Family Space

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Advances in structure-based drug design

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Structural genomics—Impact on biomedicine and drug discovery

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Structure-based drug design: From nucleic acid to membrane protein targets

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Residue Preference Mapping of Ligand Fragments in the Protein Data Bank

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A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes

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PMF Scoring Revisited

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M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility

inferredcites →https://doi.org/10.1021/jm061038aopenalex-snapshot

Propensities of Polar and Aromatic Amino Acids in Noncanonical Interactions: Nonbonded Contacts Analysis of Protein−Ligand Complexes in Crystal Structures

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A Medicinal Chemist’s Guide to Molecular Interactions

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IsoStar: A library of information about nonbonded interactions

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A Bayesian molecular interaction library

inferredcites →https://doi.org/10.1023/b:jcam.0000046819.20241.16openalex-snapshot

PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB

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Can the pharmaceutical industry reduce attrition rates?

inferredcites →https://doi.org/10.1093/nar/gkl971openalex-snapshot

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

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Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein–mononucleotide complexes

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Lessons from Structural Genomics

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Site-Directed Spectroscopic Probes of Actomyosin Structural Dynamics

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Open Babel: An open chemical toolbox

What points at this work

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

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C‐H…O hydrogen bonds in FK506‐binding protein–ligand interactions

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Landscape of protein–small ligand binding modes

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Polypharmacology rescored: Protein–ligand interaction profiles for remote binding site similarity assessment

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E2EATP: Fast and High-Accuracy Protein–ATP Binding Residue Prediction via Protein Language Model Embedding

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ATPbind: Accurate Protein–ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons

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A crystallography-based investigation of weak interactions for drug design against COVID-19

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Crystallography-based exploration of non-covalent interactions for the design and synthesis of coumarin for stronger protein binding

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Characterization of Peanut Oil by Infrared Spectroscopy with an Improved Gaussian Mixture Model

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GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

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Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints

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Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database

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A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex

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Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes

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Sequence-based prediction of function site and protein-ligand interaction by a functionally annotated domain profile database

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Large-scale analysis of ligand binding mode similarities in the PDB using interaction fingerprints

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