On the public citation graph

A method for fast energy estimation and visualization of protein-ligand interaction

0 signed · 59 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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/bip.1981.360201208openalex-snapshot

Studies of nucleotide conformations and interactions. The relative stabilities of double‐helical B‐DNA sequence isomers

inferredcites →https://doi.org/10.1002/jcc.540020311openalex-snapshot

AMBER : Assisted model building with energy refinement. A general program for modeling molecules and their interactions

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/jcc.540060510openalex-snapshot

Computer graphics in real‐time docking with energy calculation and minimization

inferredcites →https://doi.org/10.1016/0003-9861(82)90310-1openalex-snapshot

The use of crystallography, graphics, and quantitative structure-activity relationships in the analysis of the papain hydrolysis of X-phenyl hippurates

inferredcites →https://doi.org/10.1016/0005-2795(70)90258-8openalex-snapshot

Potential functions for hydrogen bond interactions I. A modified lippincott-schroeder potential function for NH⋯O interaction between peptide groups

inferredcites →https://doi.org/10.1016/0009-2614(80)85259-6openalex-snapshot

Efficient methods for solving the open-shell scf problem and for obtaining an initial guess. The “one-hamiltonian” and the “partial scf” methods

inferredcites →https://doi.org/10.1016/0022-2836(74)90163-6openalex-snapshot

Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor

inferredcites →https://doi.org/10.1016/s0021-9258(18)33497-5openalex-snapshot

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

inferredcites →https://doi.org/10.1016/s0021-9258(18)89743-5openalex-snapshot

Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim.

inferredcites →https://doi.org/10.1016/s0021-9258(18)89744-7openalex-snapshot

Dihydrofolate reductase. The stereochemistry of inhibitor selectivity.

inferredcites →https://doi.org/10.1021/bi00573a001openalex-snapshot

Picosecond dynamics of tyrosine side chains in proteins

inferredcites →https://doi.org/10.1021/j100475a014openalex-snapshot

Calculations of chemical processes in solutions

inferredcites →https://doi.org/10.1021/ja00311a071openalex-snapshot

Lone-pair directionality in hydrogen-bond potential functions for molecular mechanics calculations: the inhibition of human carbonic anhydrase II by sulfonamides

inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot

A new force field for molecular mechanical simulation of nucleic acids and proteins

inferredcites →https://doi.org/10.1021/ja00316a034openalex-snapshot

Directional hydrogen bonding to sp2- and sp3-hybridized oxygen atoms and its relevance to ligand-macromolecule interactions

inferredcites →https://doi.org/10.1021/ja00323a048openalex-snapshot

Design of inhibitors from the three-dimensional structure of alcohol dehydrogenase. Chemical synthesis and enzymic properties

inferredcites →https://doi.org/10.1021/ja00387a046openalex-snapshot

Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin

inferredcites →https://doi.org/10.1021/ja00424a009openalex-snapshot

The crystal and molecular structure of the antifolate drug trimethoprim (2,4-diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine). A neutron diffraction study

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/jm00349a003openalex-snapshot

Comparison of the inhibition of Escherichia coli and Lactobacillus casei dihydrofolate reductase by 2,4-diamino-5-(substituted-benzyl)pyrimidines: quantitative structure-activity relationships, x-ray crystallography, and computer graphics in structure-activity analysis

inferredcites →https://doi.org/10.1021/jm00349a004openalex-snapshot

Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions

inferredcites →https://doi.org/10.1021/jm00352a002openalex-snapshot

Receptor-based design of dihydrofolate reductase inhibitors: comparison of crystallographically determined enzyme binding with enzyme affinity in a series of carboxy-substituted trimethoprim analogs

inferredcites →https://doi.org/10.1021/jm00373a016openalex-snapshot

A general distance-geometry three-dimensional receptor model for diverse dihydrofolate reductase inhibitors

inferredcites →https://doi.org/10.1021/jm00381a008openalex-snapshot

Receptor-based design of dihydrofolate reductase inhibitors: comparison of crystallographically determined enzyme binding with enzyme affinity in a series of carboxy-substituted trimethoprim analogs

inferredcites →https://doi.org/10.1063/1.1742196openalex-snapshot

One-Dimensional Model of the Hydrogen Bond

inferredcites →https://doi.org/10.1073/pnas.79.12.3754openalex-snapshot

Electrostatic potential molecular surfaces.

inferredcites →https://doi.org/10.1107/s002188988301078xopenalex-snapshot

DOCKER, an interactive program for simulating protein receptor and substrate interactions

inferredcites →https://doi.org/10.1177/009286158401800206openalex-snapshot

Intermolecular Modeling Methods in Drug Design/Modeling the Mechanism of Peptide Cleavage by Thermolysin

What points at this work

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

inferred← citeshttps://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

inferred← citeshttps://doi.org/10.1002/(sici)1099-1352(199601)9:1<1::aid-jmr241>3.0.co;2-6openalex-snapshot

Automated docking of flexible ligands: Applications of autodock

inferred← citeshttps://doi.org/10.1002/9780470125885.ch1openalex-snapshot

Recent Advances in Ligand Design Methods

inferred← citeshttps://doi.org/10.1002/jcc.21625openalex-snapshot

An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method

inferred← citeshttps://doi.org/10.1002/jcc.540130412openalex-snapshot

Automated docking with grid‐based energy evaluation

inferred← citeshttps://doi.org/10.1002/prot.20931openalex-snapshot

Effective handling of induced‐fit motion in flexible docking

inferred← citeshttps://doi.org/10.1002/qua.560340709openalex-snapshot

Electrostatics and molecular recognition

inferred← citeshttps://doi.org/10.1007/978-1-349-12973-7_5openalex-snapshot

A Discussion of Various Computational Methods for Drug Design

inferred← citeshttps://doi.org/10.1007/978-1-4899-0703-5_3openalex-snapshot

Molecular Simulation of Protein-PEG Interaction

inferred← citeshttps://doi.org/10.1007/978-3-0348-7164-8_6openalex-snapshot

Generation of new-lead structures in computer-aided drug design

inferred← citeshttps://doi.org/10.1007/978-94-011-1472-1_41openalex-snapshot

New methods for 3D SAR and lead generation in computer-aided drug design

inferred← citeshttps://doi.org/10.1007/978-94-011-1472-1_95openalex-snapshot

A novel automatic docking method for flexible molecules

inferred← citeshttps://doi.org/10.1007/bf00124387openalex-snapshot

The computer program LUDI: A new method for the de novo design of enzyme inhibitors

inferred← citeshttps://doi.org/10.1007/bf00125372openalex-snapshot

GREEN: A program package for docking studies in rational drug design

inferred← citeshttps://doi.org/10.1007/bf00126441openalex-snapshot

SPROUT: A program for structure generation

inferred← citeshttps://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

inferred← citeshttps://doi.org/10.1016/b978-012178245-0/50005-6openalex-snapshot

Computer-Assisted New Lead Design

inferred← citeshttps://doi.org/10.1016/s0040-4020(01)86503-0openalex-snapshot

Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation.

inferred← citeshttps://doi.org/10.1016/s0165-7208(06)80044-9openalex-snapshot

Rational approaches to computer drug design based on drug-receptor interactions

inferred← citeshttps://doi.org/10.1021/jm030605gopenalex-snapshot

Efficient Method for High-Throughput Virtual Screening Based on Flexible Docking: Discovery of Novel Acetylcholinesterase Inhibitors

inferred← citeshttps://doi.org/10.1021/jm960728jopenalex-snapshot

Cyclic HIV-1 Protease Inhibitors Derived from Mannitol: Synthesis, Inhibitory Potencies, and Computational Predictions of Binding Affinities

inferred← citeshttps://doi.org/10.1021/jp0044476openalex-snapshot

Binding Affinities for a Series of Selective Inhibitors of Gelatinase-A Using Molecular Dynamics with a Linear Interaction Energy Approach

inferred← citeshttps://doi.org/10.1021/jp011480zopenalex-snapshot

New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model

inferred← citeshttps://doi.org/10.1021/jp0373797openalex-snapshot

Accurate Calculations of Ligand Binding Free Energies: Chiral Separation with Enantioselective Receptors

inferred← citeshttps://doi.org/10.1021/jp805007fopenalex-snapshot

Cluster Hydration Model for Binding Energy Calculations of Protein−Ligand Complexes

inferred← citeshttps://doi.org/10.1023/a:1007930623000openalex-snapshot

Ligand binding affinity prediction by linear interaction energy methods

inferred← citeshttps://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot

Molecular Recognition and Docking Algorithms

inferred← citeshttps://doi.org/10.1177/009286159402800309openalex-snapshot

Molecular Docking: A Tool for Ligand Discovery and Design

inferred← citeshttps://doi.org/10.1248/cpb.60.183openalex-snapshot

Prediction of Ligand Binding Affinity Using a Multiple-Conformations-Multiple-Protonation Scheme: Application to Estrogen Receptor .ALPHA.

inferred← citeshttps://doi.org/10.26083/tuprints-00000049openalex-snapshot

Computergestützte Strukturbestimmung biochemischer Komplexe durch einen Fuzzy Logic-basierten Algorithmus

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.