On the public citation graph
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
0 signed · 114 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.
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known work and none has been retracted — and get a dated CiteStamped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.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jcc.20022openalex-snapshot
Ligand–protein docking using a quantum stochastic tunneling optimization method
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
inferredcites →https://doi.org/10.1002/prot.10287openalex-snapshot
Algorithms for computational solvent mapping of proteins
inferredcites →https://doi.org/10.1007/978-3-662-05314-0_9openalex-snapshot
Practical Database Screening with Docking Tools
inferredcites →https://doi.org/10.1007/bf00125381openalex-snapshot
Current methods for site-directed structure generation
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1007/bf02174531openalex-snapshot
A good ligand is hard to find: Automated docking methods
inferredcites →https://doi.org/10.1016/0166-218x(88)90004-2openalex-snapshot
Determining structural similarity of chemicals using graph-theoretic indices
inferredcites →https://doi.org/10.1016/s0014-5793(99)01502-1openalex-snapshot
Anthrax lethal factor cleaves MKK3 in macrophages and inhibits the LPS/IFNγ‐induced release of NO and TNFα
inferredcites →https://doi.org/10.1016/s0021-9258(17)38364-3openalex-snapshot
Macrophages are sensitive to anthrax lethal toxin through an acid-dependent process.
inferredcites →https://doi.org/10.1016/s1359-6446(02)02483-2openalex-snapshot
Structure-based virtual screening: an overview
inferredcites →https://doi.org/10.1021/ci00009a019openalex-snapshot
Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases
inferredcites →https://doi.org/10.1021/ci00010a013openalex-snapshot
Similarity searching on CAS Registry substances. 1. Global molecular property and generic atom triangle geometric searching
inferredcites →https://doi.org/10.1021/ci00021a011openalex-snapshot
Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data
inferredcites →https://doi.org/10.1021/ci00046a002openalex-snapshot
Atom pairs as molecular features in structure-activity studies: definition and applications
inferredcites →https://doi.org/10.1021/ci00046a003openalex-snapshot
Computer code for producing Eh-pH plots of equilibrium chemical systems
inferredcites →https://doi.org/10.1021/ci00049a008openalex-snapshot
Implementation of nearest-neighbor searching in an online chemical structure search system
inferredcites →https://doi.org/10.1021/ci025531gopenalex-snapshot
Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients
inferredcites →https://doi.org/10.1021/ci025591mopenalex-snapshot
Evaluation of Similarity Measures for Searching the Dictionary of Natural Products Database
inferredcites →https://doi.org/10.1021/ci034001xopenalex-snapshot
Analysis and Display of the Size Dependence of Chemical Similarity Coefficients
inferredcites →https://doi.org/10.1021/ci9501047openalex-snapshot
Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection
inferredcites →https://doi.org/10.1021/ci950274jopenalex-snapshot
Chemical Similarity Using Physiochemical Property Descriptors
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/ci960471yopenalex-snapshot
Similarity Measures for Rational Set Selection and Analysis of Combinatorial Libraries: The Diverse Property-Derived (DPD) Approach
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm0498147openalex-snapshot
Assessment of Multiple Binding Modes in Ligand−Protein Docking
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1023/a:1007934413448openalex-snapshot
IsoStar: A library of information about nonbonded interactions
inferredcites →https://doi.org/10.1023/a:1007994827087openalex-snapshot
A branch-and-bound method for optimal atom-type assignment in de novo ligand design
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1008042711516openalex-snapshot
Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1023/a:1021242018286openalex-snapshot
A validation study on the practical use of automated de novo design
inferredcites →https://doi.org/10.1023/a:1027346709963openalex-snapshot
A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein
inferredcites →https://doi.org/10.1038/385833a0openalex-snapshot
Crystal structure of the anthrax toxin protective antigen
inferredcites →https://doi.org/10.1038/415396aopenalex-snapshot
Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
inferredcites →https://doi.org/10.1073/pnas.79.10.3162openalex-snapshot
Anthrax toxin edema factor: a bacterial adenylate cyclase that increases cyclic AMP concentrations of eukaryotic cells.
inferredcites →https://doi.org/10.1074/jbc.m301232200openalex-snapshot
Structure-based Inhibitor Discovery against Adenylyl Cyclase Toxins from Pathogenic Bacteria That Cause Anthrax and Whooping Cough
inferredcites →https://doi.org/10.1093/comjnl/20.4.359openalex-snapshot
Hierarchical grouping methods and stopping rules: an evaluation
inferredcites →https://doi.org/10.1128/iai.47.1.306-310.1985openalex-snapshot
Effects of anthrax toxin components on human neutrophils
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1198/004017002317375064openalex-snapshot
A Modification of the Jaccard–Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings
inferredcites →https://doi.org/10.2174/0929867033457809openalex-snapshot
Ligand-Protein Docking: Cancer Research at the Interface between Biology and Chemistry
inferredcites →https://doi.org/10.5281/zenodo.16435756openalex-snapshot
A Statistical Method for Evaluating Systematic Relationships
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527633326.ch6openalex-snapshot
Docking Methods for Virtual Screening: Principles and Recent Advances
inferred← citeshttps://doi.org/10.1002/9783527633326.ch7openalex-snapshot
The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1002/9783527665143.ch14openalex-snapshot
Molecular Interaction Fingerprints
inferred← citeshttps://doi.org/10.1002/aisy.202400238openalex-snapshot
ClassyPose: A Machine‐Learning Classification Model for Ligand Pose Selection Applied to Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1002/ardp.200800042openalex-snapshot
Refined Docking as a Valuable Tool for Lead Optimization: Application to Histamine H3 Receptor Antagonists
inferred← citeshttps://doi.org/10.1002/chin.200506221openalex-snapshot
Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure‐Based Drug Design.
inferred← citeshttps://doi.org/10.1002/cmdc.201100179openalex-snapshot
From Activity Cliffs to Target‐Specific Scoring Models and Pharmacophore Hypotheses
inferred← citeshttps://doi.org/10.1002/cmdc.201700505openalex-snapshot
IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1002/jcc.21814openalex-snapshot
Implementation and evaluation of a docking‐rescoring method using molecular footprint comparisons
inferred← citeshttps://doi.org/10.1002/minf.201000068openalex-snapshot
An Improved Weighted‐Residue Profile Based Method of Using Protein–Ligand Interaction Information in Increasing Hits Selection from Virtual Screening: A Study on Virtual Screening of Human GPCR A2A Receptor Antagonists
inferred← citeshttps://doi.org/10.1002/minf.201000075openalex-snapshot
Virtual Activity Profiling of Bioactive Molecules by 1D Fingerprinting
inferred← citeshttps://doi.org/10.1002/minf.201600044openalex-snapshot
A Pareto Algorithm for Efficient De Novo Design of Multi‐functional Molecules
inferred← citeshttps://doi.org/10.1002/prot.21782openalex-snapshot
A general approach for developing system‐specific functions to score protein–ligand docked complexes using support vector inductive logic programming
inferred← citeshttps://doi.org/10.1002/prp2.994openalex-snapshot
Combined docking and machine learning identify key molecular determinants of ligand pharmacological activity on β2 adrenoceptor
inferred← citeshttps://doi.org/10.1002/qsar.200510120openalex-snapshot
Current Status of Virtual Combinatorial Library Design
inferred← citeshttps://doi.org/10.1007/128_2007_144openalex-snapshot
Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand–Receptor Complexes
inferred← citeshttps://doi.org/10.1007/128_2011_182openalex-snapshot
Fragment-Based Approaches and Computer-Aided Drug Discovery
inferred← citeshttps://doi.org/10.1007/s10822-016-9923-2openalex-snapshot
A pose prediction approach based on ligand 3D shape similarity
inferred← citeshttps://doi.org/10.1007/s10822-016-9930-3openalex-snapshot
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015
inferred← citeshttps://doi.org/10.1007/s11030-012-9403-0openalex-snapshot
GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening
inferred← citeshttps://doi.org/10.1007/s12272-017-0945-7openalex-snapshot
Studies of the benzopyran class of selective COX-2 inhibitors using 3D-QSAR and molecular docking
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12346-7openalex-snapshot
2/3D Pharmacophore Definitions and Their Application
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2014.06.001openalex-snapshot
The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.08.023openalex-snapshot
Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.11.018openalex-snapshot
Structure-based protein–ligand interaction fingerprints for binding affinity prediction
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.01.001openalex-snapshot
AutoMap: A tool for analyzing protein–ligand recognition using multiple ligand binding modes
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.12.002openalex-snapshot
PLHINT: A knowledge-driven computational approach based on the intermolecular H bond interactions at the protein-ligand interface from docking solutions
inferred← citeshttps://doi.org/10.1016/j.molimm.2009.09.031openalex-snapshot
In silico analysis of antibody–carbohydrate interactions and its application to xenoreactive antibodies
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2014.05.006openalex-snapshot
Polypharmacology rescored: Protein–ligand interaction profiles for remote binding site similarity assessment
inferred← citeshttps://doi.org/10.1016/j.pharmthera.2017.02.034openalex-snapshot
The impact of in silico screening in the discovery of novel and safer drug candidates
inferred← citeshttps://doi.org/10.1016/j.pnmrs.2006.03.002openalex-snapshot
Complete relaxation and conformational exchange matrix analysis of STD-NMR spectra of ligand–receptor complexes
inferred← citeshttps://doi.org/10.1016/j.tips.2015.08.006openalex-snapshot
Advances in Computational Techniques to Study GPCR–Ligand Recognition
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00695openalex-snapshot
Prioritizing Virtual Screening with Interpretable Interaction Fingerprints
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00842openalex-snapshot
IEV2Mol: Molecular Generative Model Considering Protein–Ligand Interaction Energy Vectors
inferred← citeshttps://doi.org/10.1021/acsomega.4c05433openalex-snapshot
Bridging Structure- and Ligand-Based Virtual Screening through Fragmented Interaction Fingerprint
inferred← citeshttps://doi.org/10.1021/bi0500426openalex-snapshot
A Combined STD-NMR/Molecular Modeling Protocol for Predicting the Binding Modes of the Glycosidase Inhibitors Kifunensine and Salacinol to Golgi α-Mannosidase II
inferred← citeshttps://doi.org/10.1021/ci050420dopenalex-snapshot
Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
inferred← citeshttps://doi.org/10.1021/ci1001197openalex-snapshot
Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein−Ligand Interaction Information
inferred← citeshttps://doi.org/10.1021/ci300034xopenalex-snapshot
PROLIX: Rapid Mining of Protein–Ligand Interactions in Large Crystal Structure Databases
inferred← citeshttps://doi.org/10.1021/ci300566nopenalex-snapshot
Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs
inferred← citeshttps://doi.org/10.1021/ci600342eopenalex-snapshot
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
inferred← citeshttps://doi.org/10.1021/ci7003626openalex-snapshot
Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints
inferred← citeshttps://doi.org/10.1021/ci8000265openalex-snapshot
Homology Model-Based Virtual Screening for GPCR Ligands Using Docking and Target-Biased Scoring
inferred← citeshttps://doi.org/10.1021/ci900043ropenalex-snapshot
APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci900382eopenalex-snapshot
Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening
inferred← citeshttps://doi.org/10.1021/ci9004223openalex-snapshot
Atom-Centered Interacting Fragments and Similarity Search Applications
inferred← citeshttps://doi.org/10.1021/jm900817uopenalex-snapshot
Three-Dimensional Pharmacophore Methods in Drug Discovery
inferred← citeshttps://doi.org/10.1038/s41598-017-11924-4openalex-snapshot
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns
inferred← citeshttps://doi.org/10.1080/17460441.2021.1929921openalex-snapshot
Computational representations of protein–ligand interfaces for structure-based virtual screening
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2005.00323.xopenalex-snapshot
Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2009.00829.xopenalex-snapshot
Utilizing Target–Ligand Interaction Information in Fingerprint Searching for Ligands of Related Targets
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2009.00890.xopenalex-snapshot
Three‐Dimensional Protein–Ligand Interaction Scaling of Two‐Dimensional Fingerprints
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2010.01007.xopenalex-snapshot
Computational Methodologies for Compound Database Searching that Utilize Experimental Protein–Ligand Interaction Information
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2011.01145.xopenalex-snapshot
Role of Interactions and Volume Variation in Discriminating Active and Inactive Forms of Cyclin‐Dependent Kinase‐2 Inhibitor Complexes
inferred← citeshttps://doi.org/10.1134/s1070363210120248openalex-snapshot
Computational methods and software in computer-aided combinatorial library design
inferred← citeshttps://doi.org/10.1186/s12859-017-1750-5openalex-snapshot
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints
inferred← citeshttps://doi.org/10.1186/s13321-018-0264-0openalex-snapshot
A novel interaction fingerprint derived from per atom score contributions: exhaustive evaluation of interaction fingerprint performance in docking based virtual screening
inferred← citeshttps://doi.org/10.1186/s13321-020-00434-7openalex-snapshot
Assessing the information content of structural and protein–ligand interaction representations for the classification of kinase inhibitor binding modes via machine learning and active learning
inferred← citeshttps://doi.org/10.1186/s13321-021-00548-6openalex-snapshot
ProLIF: a library to encode molecular interactions as fingerprints
inferred← citeshttps://doi.org/10.1371/journal.pone.0069365openalex-snapshot
Re-Docking Scheme for Generating Near-Native Protein Complexes by Assembling Residue Interaction Fingerprints
inferred← citeshttps://doi.org/10.1517/17460440903317580openalex-snapshot
Advances in fragment-based drug discovery platforms
inferred← citeshttps://doi.org/10.17863/cam.36962openalex-snapshot
INTEGRATING CHEMICAL, BIOLOGICAL AND PHYLOGENETIC SPACES OF AFRICAN NATURAL PRODUCTS TO UNDERSTAND THEIR THERAPEUTIC ACTIVITY
inferred← citeshttps://doi.org/10.2174/1381612822666160224143008openalex-snapshot
Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease
inferred← citeshttps://doi.org/10.3390/ijms151120403openalex-snapshot
The Discovery of Aurora Kinase Inhibitor by Multi-Docking-Based Virtual Screening
inferred← citeshttps://doi.org/10.3390/ijms20164014openalex-snapshot
Discovery of Novel TASK-3 Channel Blockers Using a Pharmacophore-Based Virtual Screening
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch005openalex-snapshot
Protein Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch041openalex-snapshot
Protein Ligand Interaction Fingerprints
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.