On the public citation graph

Small molecule superposition: A comprehensive overview on pose scoring of the latest methods

0 signed · 128 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<520::aid-jcc2>3.0.co;2-wopenalex-snapshot

Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<553::aid-jcc3>3.0.co;2-topenalex-snapshot

Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<587::aid-jcc4>3.0.co;2-qopenalex-snapshot

Merck molecular force field. IV. conformational energies and geometries for MMFF94

inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<616::aid-jcc5>3.0.co;2-xopenalex-snapshot

Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules

inferredcites →https://doi.org/10.1002/(sici)1096-987x(19961115)17:14<1653::aid-jcc7>3.0.co;2-kopenalex-snapshot

A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

inferredcites →https://doi.org/10.1002/(sici)1099-128x(199603)10:2<107::aid-cem408>3.0.co;2-eopenalex-snapshot

Multivariate characterization of molecules for QSAR analysis

inferredcites →https://doi.org/10.1002/jcc.20770openalex-snapshot

Shapelets: Possibilities and limitations of shape‐based virtual screening

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot

CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

inferredcites →https://doi.org/10.1002/nav.3800020109openalex-snapshot

The Hungarian method for the assignment problem

inferredcites →https://doi.org/10.1007/11560500_18openalex-snapshot

Multiple Semi-flexible 3D Superposition of Drug-Sized Molecules

inferredcites →https://doi.org/10.1007/11875741_18openalex-snapshot

A Point-Matching Based Algorithm for 3D Surface Alignment of Drug-Sized Molecules

inferredcites →https://doi.org/10.1007/bf00124019openalex-snapshot

Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors

inferredcites →https://doi.org/10.1007/bf00124324openalex-snapshot

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

inferredcites →https://doi.org/10.1007/bf00141577openalex-snapshot

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

inferredcites →https://doi.org/10.1007/s10822-006-9078-7openalex-snapshot

Efficient overlay of small organic molecules using 3D pharmacophores

inferredcites →https://doi.org/10.1007/s10822-006-9082-yopenalex-snapshot

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

inferredcites →https://doi.org/10.1007/s10822-006-9087-6openalex-snapshot

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

inferredcites →https://doi.org/10.1007/s10822-011-9462-9openalex-snapshot

Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

inferredcites →https://doi.org/10.1007/s10822-012-9573-yopenalex-snapshot

Development and validation of an improved algorithm for overlaying flexible molecules

inferredcites →https://doi.org/10.1007/s10822-015-9875-yopenalex-snapshot

Avalanche for shape and feature-based virtual screening with 3D alignment

inferredcites →https://doi.org/10.1007/s10822-017-0015-8openalex-snapshot

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

inferredcites →https://doi.org/10.1007/s10822-017-0023-8openalex-snapshot

MolAlign: an algorithm for aligning multiple small molecules

inferredcites →https://doi.org/10.1007/s10822-019-00236-6openalex-snapshot

Electrostatic-field and surface-shape similarity for virtual screening and pose prediction

inferredcites →https://doi.org/10.1016/0898-5529(90)90162-2openalex-snapshot

An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap

inferredcites →https://doi.org/10.1016/j.drudis.2007.09.007openalex-snapshot

Molecule-pharmacophore superpositioning and pattern matching in computational drug design

inferredcites →https://doi.org/10.1016/j.jmgm.2004.04.004openalex-snapshot

Alignment of three-dimensional molecules using an image recognition algorithm

inferredcites →https://doi.org/10.1016/j.jmgm.2008.04.003openalex-snapshot

Pharao: Pharmacophore alignment and optimization

inferredcites →https://doi.org/10.1016/j.jmgm.2010.05.005openalex-snapshot

LigAlign: Flexible ligand-based active site alignment and analysis

inferredcites →https://doi.org/10.1021/acs.jcim.9b00020openalex-snapshot

BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping

inferredcites →https://doi.org/10.1021/ci034027oopenalex-snapshot

FLUFF-BALL, A Template-Based Grid-Independent Superposition and QSAR Technique: Validation Using a Benchmark Steroid Data Set

inferredcites →https://doi.org/10.1021/ci0342371openalex-snapshot

SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison

inferredcites →https://doi.org/10.1021/ci049641uopenalex-snapshot

Virtual Screening of Molecular Databases Using a Support Vector Machine

inferredcites →https://doi.org/10.1021/ci049885eopenalex-snapshot

LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

inferredcites →https://doi.org/10.1021/ci0503107openalex-snapshot

FLAME: A Program to Flexibly Align Molecules

inferredcites →https://doi.org/10.1021/ci050427vopenalex-snapshot

PharmID: Pharmacophore Identification Using Gibbs Sampling

inferredcites →https://doi.org/10.1021/ci1000218openalex-snapshot

pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization

inferredcites →https://doi.org/10.1021/ci100194kopenalex-snapshot

GAPE: An Improved Genetic Algorithm for Pharmacophore Elucidation

inferredcites →https://doi.org/10.1021/ci100227hopenalex-snapshot

Training a Scoring Function for the Alignment of Small Molecules

inferredcites →https://doi.org/10.1021/ci100263popenalex-snapshot

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

inferredcites →https://doi.org/10.1021/ci2002704openalex-snapshot

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring

inferredcites →https://doi.org/10.1021/ci3000369openalex-snapshot

MARS: Computing Three-Dimensional Alignments for Multiple Ligands Using Pairwise Similarities

inferredcites →https://doi.org/10.1021/ci300153dopenalex-snapshot

GRID-Based Three-Dimensional Pharmacophores I: FLAPpharm, a Novel Approach for Pharmacophore Elucidation

inferredcites →https://doi.org/10.1021/ci400020aopenalex-snapshot

An Extensive and Diverse Set of Molecular Overlays for the Validation of Pharmacophore Programs

inferredcites →https://doi.org/10.1021/ci500006dopenalex-snapshot

3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity

inferredcites →https://doi.org/10.1021/ci500618uopenalex-snapshot

PENG: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation, and Virtual Screening for Novel Ligands of LTA4H

inferredcites →https://doi.org/10.1021/ci600253eopenalex-snapshot

A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application

inferredcites →https://doi.org/10.1021/ci6003338openalex-snapshot

QUASI: A Novel Method for Simultaneous Superposition of Multiple Flexible Ligands and Virtual Screening Using Partial Similarity

inferredcites →https://doi.org/10.1021/ci600387ropenalex-snapshot

Graph-Based Molecular Alignment (GMA)

inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot

Comparison of Topological, Shape, and Docking Methods in Virtual Screening

inferredcites →https://doi.org/10.1021/ci700395fopenalex-snapshot

Technique for Generating Three-Dimensional Alignments of Multiple Ligands from One-Dimensional Alignments

inferredcites →https://doi.org/10.1021/ci8002649openalex-snapshot

Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data

inferredcites →https://doi.org/10.1021/ci800315dopenalex-snapshot

ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential

inferredcites →https://doi.org/10.1021/ci8004463openalex-snapshot

Flexible Alignment of Small Molecules Using the Penalty Method

inferredcites →https://doi.org/10.1021/ci900109nopenalex-snapshot

Elucidating Molecular Overlays from Pairwise Alignments Using a Genetic Algorithm

inferredcites →https://doi.org/10.1021/ci900204yopenalex-snapshot

LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening

inferredcites →https://doi.org/10.1021/ci900263dopenalex-snapshot

Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications

inferredcites →https://doi.org/10.1021/ci9002816openalex-snapshot

Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations

inferredcites →https://doi.org/10.1021/ci950273ropenalex-snapshot

Identification of Common Functional Configurations Among Molecules

inferredcites →https://doi.org/10.1021/ci960002wopenalex-snapshot

Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials

inferredcites →https://doi.org/10.1021/ci980213wopenalex-snapshot

Quadratic Shape Descriptors. 1. Rapid Superposition of Dissimilar Molecules Using Geometrically Invariant Surface Descriptors

inferredcites →https://doi.org/10.1021/ci9900682openalex-snapshot

Multiple Flexible Alignment with SEAL: A Study of Molecules Acting on the Colchicine Binding Site

inferredcites →https://doi.org/10.1021/j100011a016openalex-snapshot

A Gaussian Description of Molecular Shape

inferredcites →https://doi.org/10.1021/ja00066a004openalex-snapshot

3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: a comparison of CoMFA models based on deduced and experimentally determined active site geometries

inferredcites →https://doi.org/10.1021/ja00194a034openalex-snapshot

A new approach to probing conformational space with molecular mechanics: random incremental pulse search

inferredcites →https://doi.org/10.1021/ja01612a111openalex-snapshot

Molecular Theory of Gases and Liquids.

inferredcites →https://doi.org/10.1021/jm0002634openalex-snapshot

Flexible Alignment of Small Molecules

inferredcites →https://doi.org/10.1021/jm00093a021openalex-snapshot

Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogs

inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

inferredcites →https://doi.org/10.1021/jm0210616openalex-snapshot

Field Interaction and Geometrical Overlap: A New Simplex and Experimental Design Based Computational Procedure for Superposing Small Ligand Molecules

inferredcites →https://doi.org/10.1021/jm030580lopenalex-snapshot

The PDBbind Database: Collection of Binding Affinities for Protein−Ligand Complexes with Known Three-Dimensional Structures

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

inferredcites →https://doi.org/10.1021/jm040163oopenalex-snapshot

A Shape-Based 3-D Scaffold Hopping Method and Its Application to a Bacterial Protein−Protein Interaction

inferredcites →https://doi.org/10.1021/jm048957qopenalex-snapshot

The PDBbind Database: Methodologies and Updates

inferredcites →https://doi.org/10.1021/jm049123aopenalex-snapshot

BRUTUS: Optimization of a Grid-Based Similarity Function for Rigid-Body Molecular Superposition. 1. Alignment and Virtual Screening Applications

inferredcites →https://doi.org/10.1021/jm0497141openalex-snapshot

A Comparison of Methods for Modeling Quantitative Structure−Activity Relationships

inferredcites →https://doi.org/10.1021/jm0498349openalex-snapshot

Hydrogen Bonding Interactions of Covalently Bonded Fluorine Atoms: From Crystallographic Data to a New Angular Function in the GRID Force Field

inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot

Comparison of Shape-Matching and Docking as Virtual Screening Tools

inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

inferredcites →https://doi.org/10.1021/jm900818sopenalex-snapshot

Molecular Shape and Medicinal Chemistry: A Perspective

inferredcites →https://doi.org/10.1021/jm981037lopenalex-snapshot

F lex S: A Method for Fast Flexible Ligand Superposition

inferredcites →https://doi.org/10.1023/a:1007959729800openalex-snapshot

Time-efficient flexible superposition of medium-sized molecules

inferredcites →https://doi.org/10.1023/a:1008034527445openalex-snapshot

Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs

inferredcites →https://doi.org/10.1023/a:1008100132405openalex-snapshot

Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition

inferredcites →https://doi.org/10.1023/a:1008167930625openalex-snapshot

A novel method of aligning molecules by local surface shape similarity

inferredcites →https://doi.org/10.1023/a:1008194019144openalex-snapshot

Computational methods for the structural alignment of molecules

inferredcites →https://doi.org/10.1023/a:1011102129244openalex-snapshot

slate: A method for the superposition of flexible ligands

inferredcites →https://doi.org/10.1023/a:1011921423829openalex-snapshot

FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules

inferredcites →https://doi.org/10.1023/a:1021954728347openalex-snapshot

A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP

inferredcites →https://doi.org/10.1023/a:1024503712135openalex-snapshot

Fast 3D molecular superposition and similarity search in databases of flexible molecules

inferredcites →https://doi.org/10.1038/d41586-020-03348-4openalex-snapshot

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures

inferredcites →https://doi.org/10.1038/nrd1718openalex-snapshot

Poly(ADP-ribose) polymerase and the therapeutic effects of its inhibitors

inferredcites →https://doi.org/10.1089/cmb.2007.0130openalex-snapshot

Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules

inferredcites →https://doi.org/10.1090/s0025-5718-1970-0258249-6openalex-snapshot

A Family of Variable-Metric Methods Derived by Variational Means

inferredcites →https://doi.org/10.1093/bioinformatics/btaa089openalex-snapshot

InterLig: improved ligand-based virtual screening using topologically independent structural alignments

inferredcites →https://doi.org/10.1093/bioinformatics/btu692openalex-snapshot

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening

inferredcites →https://doi.org/10.1093/bioinformatics/bty081openalex-snapshot

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening

inferredcites →https://doi.org/10.1093/bioinformatics/bty587openalex-snapshot

Topology independent structural matching discovers novel templates for protein interfaces

inferredcites →https://doi.org/10.1093/comjnl/13.3.317openalex-snapshot

A new approach to variable metric algorithms

inferredcites →https://doi.org/10.1093/comjnl/45.6.631openalex-snapshot

RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs

inferredcites →https://doi.org/10.1093/imamat/6.1.76openalex-snapshot

The Convergence of a Class of Double-rank Minimization Algorithms 1. General Considerations

inferredcites →https://doi.org/10.1093/imamat/6.3.222openalex-snapshot

The Convergence of a Class of Double-rank Minimization Algorithms

inferredcites →https://doi.org/10.1093/nar/gkn187openalex-snapshot

PharmaGist: a webserver for ligand-based pharmacophore detection

inferredcites →https://doi.org/10.1107/s0567739476001873openalex-snapshot

A solution for the best rotation to relate two sets of vectors

inferredcites →https://doi.org/10.1107/s0567739477000862openalex-snapshot

A different best rigid-body molecular fit routine

inferredcites →https://doi.org/10.1109/mci.2006.329691openalex-snapshot

Ant colony optimization

inferredcites →https://doi.org/10.1111/j.1747-0285.2006.00384.xopenalex-snapshot

PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching

inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00605.xopenalex-snapshot

Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

inferredcites →https://doi.org/10.1186/s12859-015-0874-8openalex-snapshot

MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

inferredcites →https://doi.org/10.3389/fchem.2018.00315openalex-snapshot

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

inferredcites →https://doi.org/10.5860/choice.27-0916openalex-snapshot

Distance geometry and molecular conformation

What points at this work

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

inferred← citeshttps://doi.org/10.1002/pro.5027openalex-snapshot

MAGPIE: An interactive tool for visualizing and analyzing protein–ligand interactions

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.aichem.2024.100077openalex-snapshot

Molecular similarity: Theory, applications, and perspectives

inferred← citeshttps://doi.org/10.1016/j.bioorg.2024.107285openalex-snapshot

Discovery of macrocyclic CDK2/4/6 inhibitors with improved potency and DMPK properties through a highly efficient macrocyclic drug design platform

inferred← citeshttps://doi.org/10.1016/j.bioorg.2026.110400openalex-snapshot

Radioiodination, biological distribution, and docking study of diosmetin as a potential radiotracer for infection detection

inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.116395openalex-snapshot

Design, synthesis and evaluation of a pyrazolo[3,4-d]pyrimidine derivative as a novel and potent TGFβ1R1 inhibitor

inferred← citeshttps://doi.org/10.1016/j.lwt.2024.116305openalex-snapshot

Molecular recognition mechanisms of vanillin and high-throughput screening of its analogs based on olfactory receptors

inferred← citeshttps://doi.org/10.1016/j.sbi.2023.102578openalex-snapshot

Navigating large chemical spaces in early-phase drug discovery

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00861openalex-snapshot

Benchmark Data Set of Crystalline Organic Semiconductors

inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00399openalex-snapshot

Machine Learning Guided AQFEP: A Fast and Efficient Absolute Free Energy Perturbation Solution for Virtual Screening

inferred← citeshttps://doi.org/10.1021/acs.jpca.5c06391openalex-snapshot

Benchmarking Structures and UV–Vis Spectra of Iron Complexes Against Experimental Data

inferred← citeshttps://doi.org/10.1093/bib/bbaf620openalex-snapshot

Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders

inferred← citeshttps://doi.org/10.11606/t.59.2023.tde-13062023-075448openalex-snapshot

Planejamento computacional e avaliação biológica de inibidores alostéricos de glicogênio sintase cinase 3-β com interesse na doença de Alzheimer

inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-cs3wbopenalex-snapshot

Molecular Similarity: Theory, Applications, and Perspectives

inferred← citeshttps://doi.org/10.3390/ddc2020017openalex-snapshot

Virtual Screening Algorithms in Drug Discovery: A Review Focused on Machine and Deep Learning Methods

inferred← citeshttps://doi.org/10.3390/ecsoc-28-20197openalex-snapshot

Study of the Stability, Solubility and Geometry of the Complex of Inclusion β-CD with Nimesulide by Computer Chemistry Methods

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.