On the public citation graph

Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions

0 signed · 104 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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)1097-0134(199709)29:1<32::aid-prot3>3.0.co;2-hopenalex-snapshot

Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs

inferredcites →https://doi.org/10.1002/(sici)1097-0134(19981001)33:1<62::aid-prot6>3.0.co;2-nopenalex-snapshot

A new method for predicting binding free energy between receptor and ligand

inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000515)39:3<261::aid-prot90>3.0.co;2-4openalex-snapshot

Side-chain flexibility in proteins upon ligand binding

inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000801)40:2<185::aid-prot20>3.0.co;2-xopenalex-snapshot

Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK

inferredcites →https://doi.org/10.1002/(sici)1521-3838(199810)17:05<427::aid-qsar427>3.0.co;2-oopenalex-snapshot

Multiple Binding Modes in 3D-QSAR: Microbial Degradation of Polychlorinated Biphenyls

inferredcites →https://doi.org/10.1002/0471224413.ch1openalex-snapshot

Small Molecule Docking and Scoring

inferredcites →https://doi.org/10.1002/0471266949openalex-snapshot

Burger's Medicinal Chemistry and Drug Discovery

inferredcites →https://doi.org/10.1002/0471266949.bmc007openalex-snapshot

Docking and Scoring Functions/Virtual Screening

inferredcites →https://doi.org/10.1002/1097-0134(2000)41:4+<63::aid-prot60>3.0.co;2-6openalex-snapshot

Structural stability of binding sites: Consequences for binding affinity and allosteric effects

inferredcites →https://doi.org/10.1002/1521-3773(20020802)41:15<2644::aid-anie2644>3.0.co;2-oopenalex-snapshot

Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors

inferredcites →https://doi.org/10.1002/1521-3838(200210)21:4<382::aid-qsar382>3.0.co;2-lopenalex-snapshot

Multidimensional QSAR: Moving from three- to five-dimensional concepts

inferredcites →https://doi.org/10.1002/bip.360221211openalex-snapshot

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

inferredcites →https://doi.org/10.1002/bmb.2003.494031059996openalex-snapshot

Structural bioinformatics

inferredcites →https://doi.org/10.1002/cem.729openalex-snapshot

A systematic evaluation of the benefits and hazards of variable selection in latent variable regression. Part II. Practical applications

inferredcites →https://doi.org/10.1002/jcc.10128openalex-snapshot

Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation

inferredcites →https://doi.org/10.1002/jcc.20175openalex-snapshot

A scoring function for docking ligands to low‐resolution protein structures

inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot

The Amber biomolecular simulation programs

inferredcites →https://doi.org/10.1002/prot.340040110openalex-snapshot

Crystallization and preliminary investigation of single crystals of deoxyuidine triphosphate nucleotidohydrolase from Escherichia coli

inferredcites →https://doi.org/10.1002/prot.340170404openalex-snapshot

Recognition of errors in three‐dimensional structures of proteins

inferredcites →https://doi.org/10.1006/jmbi.1993.1626openalex-snapshot

Comparative Protein Modelling by Satisfaction of Spatial Restraints

inferredcites →https://doi.org/10.1006/jmbi.1995.0567openalex-snapshot

Calculation of Relative Binding Free Energies and Configurational Entropies: A Structural and Thermodynamic Analysis of the Nature of Non-polar Binding of Thrombin Inhibitors Based on Hirudin55–65

inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot

Knowledge-based scoring function to predict protein-ligand interactions

inferredcites →https://doi.org/10.1006/jmbi.2000.4453openalex-snapshot

Docking ligands onto binding site representations derived from proteins built by homology modelling

inferredcites →https://doi.org/10.1007/0-306-46858-1_16openalex-snapshot

A Critical Review of Recent CoMFA Applications

inferredcites →https://doi.org/10.1007/0-306-46858-1_5openalex-snapshot

GOLPE-Guided Region Selection

inferredcites →https://doi.org/10.1007/0-306-46883-2_8openalex-snapshot

Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function

inferredcites →https://doi.org/10.1007/978-94-011-1350-2_12openalex-snapshot

Comparative molecular field analysis (CoMFA)

inferredcites →https://doi.org/10.1007/bf00124364openalex-snapshot

Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA

inferredcites →https://doi.org/10.1007/bf00124456openalex-snapshot

MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry

inferredcites →https://doi.org/10.1007/s10822-006-9100-0openalex-snapshot

Pushing the boundaries of 3D-QSAR

inferredcites →https://doi.org/10.1016/j.ddtec.2004.11.018openalex-snapshot

Using 3D protein structures to derive 3D-QSARs

inferredcites →https://doi.org/10.1016/s0022-2836(02)01409-2openalex-snapshot

Utilising Structural Knowledge in Drug Design Strategies: Applications Using Relibase

inferredcites →https://doi.org/10.1016/s0026-895x(24)23192-8openalex-snapshot

Accommodating Protein Flexibility in Computational Drug Design,

inferredcites →https://doi.org/10.1016/s0223-5234(00)00108-2openalex-snapshot

Validation of protein-based alignment in 3D quantitative structure–activity relationships with CoMFA models

inferredcites →https://doi.org/10.1016/s1093-3263(01)00123-1openalex-snapshot

Beware of q2!

inferredcites →https://doi.org/10.1016/s1359-6446(02)02292-4openalex-snapshot

Statistical intelligence: effective analysis of high-density microarray data

inferredcites →https://doi.org/10.1016/s1359-6446(02)02483-2openalex-snapshot

Structure-based virtual screening: an overview

inferredcites →https://doi.org/10.1016/s1367-5931(02)00341-1openalex-snapshot

Protein flexibility and drug design: how to hit a moving target

inferredcites →https://doi.org/10.1021/ci010025xopenalex-snapshot

How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment

inferredcites →https://doi.org/10.1021/ci0340714openalex-snapshot

Quantitative Structure-Based Design: Formalism and Application of Receptor-Dependent RD-4D-QSAR Analysis to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase

inferredcites →https://doi.org/10.1021/ci034100aopenalex-snapshot

Multimode Ligand Binding in Receptor Site Modeling: Implementation in CoMFA

inferredcites →https://doi.org/10.1021/ci049733jopenalex-snapshot

An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

inferredcites →https://doi.org/10.1021/ci990019popenalex-snapshot

Structure Based Prediction of Binding Affinity of Human Immunodeficiency Virus-1 Protease Inhibitors

inferredcites →https://doi.org/10.1021/ja00092a006openalex-snapshot

Multiple Highly Diverse Structures Complementary to Enzyme Binding Sites: Results of Extensive Application of a de Novo Design Method Incorporating Combinatorial Growth

inferredcites →https://doi.org/10.1021/ja00226a005openalex-snapshot

Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins

inferredcites →https://doi.org/10.1021/ja9718937openalex-snapshot

Construction of 3D-QSAR Models Using the 4D-QSAR Analysis Formalism

inferredcites →https://doi.org/10.1021/jm00002a012openalex-snapshot

A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site

inferredcites →https://doi.org/10.1021/jm00007a003openalex-snapshot

Cross-Validated R2-Guided Region Selection for Comparative Molecular Field Analysis: A Simple Method To Achieve Consistent Results

inferredcites →https://doi.org/10.1021/jm00014a020openalex-snapshot

Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis

inferredcites →https://doi.org/10.1021/jm000255nopenalex-snapshot

Estimation of Binding Affinities for HEPT and Nevirapine Analogues with HIV-1 Reverse Transcriptase via Monte Carlo Simulations

inferredcites →https://doi.org/10.1021/jm00033a014openalex-snapshot

The Use of the GRID Program in the 3-D QSAR Analysis of a Series of Calcium-Channel Agonists

inferredcites →https://doi.org/10.1021/jm000405uopenalex-snapshot

Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo Simulations

inferredcites →https://doi.org/10.1021/jm00042a012openalex-snapshot

Comparative Molecular Field Analysis Using GRID Force-Field and GOLPE Variable Selection Methods in a Study of Inhibitors of Glycogen Phosphorylase b

inferredcites →https://doi.org/10.1021/jm00050a010openalex-snapshot

Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

inferredcites →https://doi.org/10.1021/jm001070jopenalex-snapshot

Comparative Binding Energy (COMBINE) Analysis of Influenza Neuraminidase−Inhibitor Complexes

inferredcites →https://doi.org/10.1021/jm0100279openalex-snapshot

Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System

inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot

Comparative Evaluation of 11 Scoring Functions for Molecular Docking

inferredcites →https://doi.org/10.1021/jm020808popenalex-snapshot

DrugScore Meets CoMFA: Adaptation of Fields for Molecular Comparison (AFMoC) or How to Tailor Knowledge-Based Pair-Potentials to a Particular Protein

inferredcites →https://doi.org/10.1021/jm025507uopenalex-snapshot

Docking into Knowledge-Based Potential Fields: A Comparative Evaluation of DrugScore

inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot

Assessing Scoring Functions for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm040835aopenalex-snapshot

Derivation and Validation of Toxicophores for Mutagenicity Prediction

inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot

Validation and Use of the MM-PBSA Approach for Drug Discovery

inferredcites →https://doi.org/10.1021/jm0491501openalex-snapshot

AFMoC Enhances Predictivity of 3D QSAR: A Case Study with DOXP-reductoisomerase

inferredcites →https://doi.org/10.1021/jm049187lopenalex-snapshot

Structural Requirements for Factor Xa Inhibition by 3-Oxybenzamides with Neutral P1 Substituents: Combining X-ray Crystallography, 3D-QSAR, and Tailored Scoring Functions

inferredcites →https://doi.org/10.1021/jm049756popenalex-snapshot

Soft Docking and Multiple Receptor Conformations in Virtual Screening

inferredcites →https://doi.org/10.1021/jm050114ropenalex-snapshot

Improving Binding Mode Predictions by Docking into Protein-Specifically Adapted Potential Fields

inferredcites →https://doi.org/10.1021/jm940778topenalex-snapshot

An Approach to Rapid Estimation of Relative Binding Affinities of Enzyme Inhibitors: Application to Peptidomimetic Inhibitors of the Human Immunodeficiency Virus Type 1 Protease

inferredcites →https://doi.org/10.1021/jm980515popenalex-snapshot

Prediction of Ligand−Receptor Binding Thermodynamics by Free Energy Force Field Three-Dimensional Quantitative Structure−Activity Relationship Analysis: Applications to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase

inferredcites →https://doi.org/10.1021/jm981062ropenalex-snapshot

Three-Dimensional Quantitative Structure−Activity Relationship Analyses Using Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis To Elucidate Selectivity Differences of Inhibitors Binding to Trypsin, Thrombin, and Factor Xa

inferredcites →https://doi.org/10.1021/jm990322hopenalex-snapshot

Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot

Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

inferredcites →https://doi.org/10.1021/jm9910775openalex-snapshot

Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins

inferredcites →https://doi.org/10.1021/tx060188lopenalex-snapshot

Structural Determinants of Binding of Aromates to Extracellular Matrix: A Multi-Species Multi-Mode CoMFA Study

inferredcites →https://doi.org/10.1023/a:1008040323669openalex-snapshot

Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model

inferredcites →https://doi.org/10.1023/a:1023888813526openalex-snapshot

Development of biologically active compounds by combining 3D QSAR and structure-based design methods

inferredcites →https://doi.org/10.1023/a:1024557113083openalex-snapshot

In silico rationalization of the structural and physicochemical requirements for photobiological activity in angelicine derivatives and their heteroanalogues

inferredcites →https://doi.org/10.1023/a:1025386326946openalex-snapshot

Rational selection of training and test sets for the development of validated QSAR models

inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot

Implications of protein flexibility for drug discovery

inferredcites →https://doi.org/10.1038/nsb1094-735openalex-snapshot

Prediction of new serine proteinase inhibitors

inferredcites →https://doi.org/10.1093/nar/gkg500openalex-snapshot

Multiple sequence alignment with the Clustal series of programs

inferredcites →https://doi.org/10.1107/s0021889892009282openalex-snapshot

The FROG PC series: programs for electron-density and model investigations for proteins

inferredcites →https://doi.org/10.1107/s0021889892009944openalex-snapshot

PROCHECK: a program to check the stereochemical quality of protein structures

inferredcites →https://doi.org/10.1107/s0907444994011686openalex-snapshot

Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes

inferredcites →https://doi.org/10.1124/mol.57.3.474openalex-snapshot

A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics

inferredcites →https://doi.org/10.1126/science.287.5460.1960openalex-snapshot

Drug Discovery: A Historical Perspective

inferredcites →https://doi.org/10.1126/science.287.5460.1964openalex-snapshot

Target-Oriented and Diversity-Oriented Organic Synthesis in Drug Discovery

inferredcites →https://doi.org/10.1137/0905052openalex-snapshot

The Collinearity Problem in Linear Regression. The Partial Least Squares (PLS) Approach to Generalized Inverses

inferredcites →https://doi.org/10.3109/14756369509040683openalex-snapshot

Structure-Actmty Relationships of Inhibitors Derived from 3-Amidinophenylalanine

What points at this work

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

inferred← citeshttps://doi.org/10.1002/med.21483openalex-snapshot

Computational chemical biology and drug design: Facilitating protein structure, function, and modulation studies

inferred← citeshttps://doi.org/10.1002/minf.201200015openalex-snapshot

From Hansch‐Fujita Analysis to AFMoC: A Road to Structure‐Based QSAR

inferred← citeshttps://doi.org/10.1007/978-3-031-81728-1_25openalex-snapshot

Transformation of QSAR by AI and ML

inferred← citeshttps://doi.org/10.1007/s00044-014-1072-3openalex-snapshot

Quantitative structure–activity relationship (QSAR) studies as strategic approach in drug discovery

inferred← citeshttps://doi.org/10.1007/s10822-010-9320-1openalex-snapshot

Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12353-4openalex-snapshot

Lessons and Successes in the Use of Molecular Fields

inferred← citeshttps://doi.org/10.1016/b978-0-12-801505-6.00008-9openalex-snapshot

Introduction to 3D-QSAR

inferred← citeshttps://doi.org/10.1016/j.drudis.2009.03.013openalex-snapshot

Targeted scoring functions for virtual screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00079openalex-snapshot

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM

inferred← citeshttps://doi.org/10.1021/ci100182copenalex-snapshot

Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions

inferred← citeshttps://doi.org/10.1021/ci800015sopenalex-snapshot

An Integrated Approach to Ligand- and Structure-Based Drug Design: Development and Application to a Series of Serine Protease Inhibitors

inferred← citeshttps://doi.org/10.1038/srep27333openalex-snapshot

Chalcone-based Selective Inhibitors of a C4 Plant Key Enzyme as Novel Potential Herbicides

inferred← citeshttps://doi.org/10.1517/17460441003652959openalex-snapshot

The GRID/CPCA approach in drug discovery

inferred← citeshttps://doi.org/10.2174/1386207323666200324173231openalex-snapshot

Quantitative Structure-Activity Relationship (QSAR) Studies for the Inhibition of MAOs

inferred← citeshttps://doi.org/10.2174/156802610790232260openalex-snapshot

3D-QSAR in Drug Design - A Review

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.