On the public citation graph

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

inferredcites →https://doi.org/10.1002/jcc.10061openalex-snapshot

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

inferredcites →https://doi.org/10.1002/jcc.20082openalex-snapshot

Empirical force fields for biological macromolecules: Overview and issues

inferredcites →https://doi.org/10.1002/jcc.20084openalex-snapshot

UCSF Chimera—A visualization system for exploratory research and analysis

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/pro.5560051206openalex-snapshot

Protein clefts in molecular recognition and function.

inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot

A protein–protein docking benchmark

inferredcites →https://doi.org/10.1002/prot.20680openalex-snapshot

An intuitive approach to measuring protein surface curvature

inferredcites →https://doi.org/10.1002/prot.20897openalex-snapshot

On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites

inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot

A geometric approach to macromolecule-ligand interactions

inferredcites →https://doi.org/10.1016/0263-7855(88)80054-7openalex-snapshot

The MIDAS display system

inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot

VMD: Visual molecular dynamics

inferredcites →https://doi.org/10.1016/j.bmcl.2006.09.038openalex-snapshot

Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure

inferredcites →https://doi.org/10.1016/j.cbpa.2004.06.006openalex-snapshot

Emerging classes of protein–protein interaction inhibitors and new tools for their development

inferredcites →https://doi.org/10.1016/j.cbpa.2006.04.002openalex-snapshot

Structure-based virtual screening of chemical libraries for drug discovery

inferredcites →https://doi.org/10.1016/j.jmb.2004.02.040openalex-snapshot

ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

inferredcites →https://doi.org/10.1016/j.jmb.2005.07.074openalex-snapshot

High Affinity Targets of Protein Kinase Inhibitors Have Similar Residues at the Positions Energetically Important for Binding

inferredcites →https://doi.org/10.1016/s0014-827x(02)01211-9openalex-snapshot

Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design

inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1

inferredcites →https://doi.org/10.1016/s0959-440x(03)00075-7openalex-snapshot

Ligand binding: functional site location, similarity and docking

inferredcites →https://doi.org/10.1016/s0968-0896(00)00180-2openalex-snapshot

Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets

inferredcites →https://doi.org/10.1021/bi00053a005openalex-snapshot

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV

inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot

Reoptimization of MDL Keys for Use in Drug Discovery

inferredcites →https://doi.org/10.1021/ci010366aopenalex-snapshot

Is There a Difference between Leads and Drugs? A Historical Perspective

inferredcites →https://doi.org/10.1021/ci020055fopenalex-snapshot

Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening

inferredcites →https://doi.org/10.1021/jm000467kopenalex-snapshot

Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data

inferredcites →https://doi.org/10.1021/jm030470eopenalex-snapshot

Identification of Non-Phosphate-Containing Small Molecular Weight Inhibitors of the Tyrosine Kinase p56 Lck SH2 Domain via in Silico Screening against the pY + 3 Binding Site

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

Assessing Scoring Functions for Protein−Ligand Interactions

inferredcites →https://doi.org/10.1021/jm0497038openalex-snapshot

Identification and Characterization of Small Molecule Inhibitors of the Calcium-Dependent S100B−p53 Tumor Suppressor Interaction

inferredcites →https://doi.org/10.1021/jm0501174openalex-snapshot

Identification of Novel Extracellular Signal-Regulated Kinase Docking Domain Inhibitors

inferredcites →https://doi.org/10.1021/jp9610776openalex-snapshot

Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects

inferredcites →https://doi.org/10.1021/jp972682ropenalex-snapshot

New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions

inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

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:1011115820450openalex-snapshot

DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

inferredcites →https://doi.org/10.1023/b:jcam.0000046820.08222.83openalex-snapshot

Molecular modelling prediction of ligand binding site flexibility

inferredcites →https://doi.org/10.1073/pnas.93.1.13openalex-snapshot

Principles of protein-protein interactions.

inferredcites →https://doi.org/10.1073/pnas.97.10.5113openalex-snapshot

(4-Aminomethyl)phenylguanidine derivatives as nonpeptidic highly selective inhibitors of human urokinase

inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot

Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes

inferredcites →https://doi.org/10.1088/1478-3975/2/2/s01openalex-snapshot

Prediction of physical protein–protein interactions

inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkl454openalex-snapshot

Protein binding site prediction using an empirical scoring function

inferredcites →https://doi.org/10.1107/s0021889883010985openalex-snapshot

Analytical molecular surface calculation

inferredcites →https://doi.org/10.1110/ps.0202302openalex-snapshot

Efficient docking of peptides to proteins without prior knowledge of the binding site

inferredcites →https://doi.org/10.1126/science.6879170openalex-snapshot

Solvent-Accessible Surfaces of Proteins and Nucleic Acids

inferredcites →https://doi.org/10.1385/1-59745-116-9:207openalex-snapshot

Prediction of Protein-Protein Interaction Based on Structure

inferredcites →https://doi.org/10.2174/0929867043455800openalex-snapshot

Improving the Understanding of Human Genetic Diseases Through Predictions of Protein Structures and Protein-Protein Interaction Sites

inferredcites →https://doi.org/10.2174/1389203033487171openalex-snapshot

Nano-Mechanical Methods in Biochemistry using Atomic Force Microscopy

inferredcites →https://doi.org/10.2174/1389203033487225openalex-snapshot

Computational Analyses of High-Throughput Protein-Protein Interaction Data

inferredcites →https://doi.org/10.2174/138920305774329313openalex-snapshot

Computational Methods for Protein-Protein Interaction and their Application

inferredcites →https://doi.org/10.2174/138920305774329322openalex-snapshot

Pattern Recognition Methods for Protein Functional Site Prediction

inferredcites →https://doi.org/10.2174/138920306778559386openalex-snapshot

Methods for the Prediction of Protein-Ligand Binding Sites for Structure-Based Drug Design and Virtual Ligand Screening.

inferredcites →https://doi.org/10.2174/1389557043403675openalex-snapshot

Virtual Screening in Structure-Based Drug Discovery

inferredcites →https://doi.org/10.2174/156802607779318334openalex-snapshot

Computational Identification of Inhibitors of Protein-Protein Interactions

inferredcites →https://doi.org/10.2174/157340606776056151openalex-snapshot

Mitogen Activated Protein (MAP) Kinases: Development of ATP and Non- ATP Dependent Inhibitors

inferredcites →https://doi.org/10.5860/choice.26-6311openalex-snapshot

Adaptive pattern recognition and neural networks

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9783527645947.ch15openalex-snapshot

Prospects of Modulating Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1002/9783527683604.ch09openalex-snapshot

Computational Methods to Support Fragment‐based Drug Discovery

inferred← citeshttps://doi.org/10.1002/bip.22130openalex-snapshot

Outside‐binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1

inferred← citeshttps://doi.org/10.1002/jcc.21571openalex-snapshot

Structure‐based quantitative structure‐activity relationship studies of checkpoint kinase 1 inhibitors

inferred← citeshttps://doi.org/10.1002/jcc.23026openalex-snapshot

Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery

inferred← citeshttps://doi.org/10.1002/jmr.984openalex-snapshot

Computational approaches to identifying and characterizing protein binding sites for ligand design

inferred← citeshttps://doi.org/10.1002/pro.540openalex-snapshot

Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library

inferred← citeshttps://doi.org/10.1007/978-1-4939-6634-9_5openalex-snapshot

Computer-Aided Drug Design Methods

inferred← citeshttps://doi.org/10.1007/978-1-4939-9145-7_5openalex-snapshot

In Silico Target Druggability Assessment: From Structural to Systemic Approaches

inferred← citeshttps://doi.org/10.1007/978-1-62703-311-4_10openalex-snapshot

Structure-Based Target Druggability Assessment

inferred← citeshttps://doi.org/10.1007/978-3-030-48283-1_5openalex-snapshot

Developing Kinase Inhibitors Using Computer-Aided Drug Design Approaches

inferred← citeshttps://doi.org/10.1007/s00894-014-2525-9openalex-snapshot

Targeting a cluster of arginine residues of neuraminidase to avoid oseltamivir resistance in influenza A (H1N1): a theoretical study

inferred← citeshttps://doi.org/10.1007/s00894-015-2835-6openalex-snapshot

Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase

inferred← citeshttps://doi.org/10.1007/s10969-011-9110-6openalex-snapshot

Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures

inferred← citeshttps://doi.org/10.1016/b978-0-443-15280-1.00011-xopenalex-snapshot

Principles of computational drug designing and drug repurposing—An algorithmic approach

inferred← citeshttps://doi.org/10.1016/j.cbpa.2011.05.020openalex-snapshot

Structure-based druggability assessment — identifying suitable targets for small molecule therapeutics

inferred← citeshttps://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

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/10.1021/acsomega.3c01621openalex-snapshot

A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2

inferred← citeshttps://doi.org/10.1021/ci100241yopenalex-snapshot

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

inferred← citeshttps://doi.org/10.1021/ci100265xopenalex-snapshot

Protein−Protein Binding Site Prediction by Local Structural Alignment

inferred← citeshttps://doi.org/10.1021/ci100312topenalex-snapshot

Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

inferred← citeshttps://doi.org/10.1021/ci200193zopenalex-snapshot

AADS- An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors

inferred← citeshttps://doi.org/10.1021/ci400750xopenalex-snapshot

Computational Method To Identify Druggable Binding Sites That Target Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1021/ci8000315openalex-snapshot

Protein Surface Conservation in Binding Sites

inferred← citeshttps://doi.org/10.1021/ci900397topenalex-snapshot

Protein Pockets: Inventory, Shape, and Comparison

inferred← citeshttps://doi.org/10.1021/jm4014357openalex-snapshot

Rapid Identification of Ligand-Binding Sites by Using an Assignment-Free NMR Approach

inferred← citeshttps://doi.org/10.1021/jp404582wopenalex-snapshot

Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces. I. Sampling and Focusing

inferred← citeshttps://doi.org/10.1039/d1nj00619copenalex-snapshot

Supramolecular assemblies involving biologically relevant antiparallel π-stacking and unconventional solvent driven structural topology in maleato and fumarato bridged Zn( ii ) coordination polymers: antiproliferative evaluation and theoretical studies

inferred← citeshttps://doi.org/10.1042/bj20131571openalex-snapshot

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf

inferred← citeshttps://doi.org/10.1080/07391102.2020.1731603openalex-snapshot

Natural chemical entities from Arisaema genus might be a promising break-through against Japanese encephalitis virus infection: a molecular docking and dynamics approach

inferred← citeshttps://doi.org/10.1093/bioinformatics/btt644openalex-snapshot

Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models

inferred← citeshttps://doi.org/10.1093/hmg/ddu341openalex-snapshot

Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models

inferred← citeshttps://doi.org/10.1111/cbdd.12066openalex-snapshot

Expanding the Number of ‘Druggable’ Targets: Non‐Enzymes and Protein–Protein Interactions

inferred← citeshttps://doi.org/10.1142/s0219633608004155openalex-snapshot

POSE SCALING: GEOMETRICAL ASSESSMENT OF LIGAND BINDING POSES

inferred← citeshttps://doi.org/10.1158/0008-5472.can-16-0061openalex-snapshot

The Small Molecule IMR-1 Inhibits the Notch Transcriptional Activation Complex to Suppress Tumorigenesis

inferred← citeshttps://doi.org/10.1186/1471-2105-10-168openalex-snapshot

Fpocket: An open source platform for ligand pocket detection

inferred← citeshttps://doi.org/10.1186/1471-2105-12-s14-s9openalex-snapshot

A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information

inferred← citeshttps://doi.org/10.1201/b18799-4openalex-snapshot

Force-Field Representation of Biomolecular Systems

inferred← citeshttps://doi.org/10.1201/b18799-7openalex-snapshot

- Force-Field Representation of Biomolecular Systems

inferred← citeshttps://doi.org/10.1517/17460441.2010.497534openalex-snapshot

De novodesign: balancing novelty and confined chemical space

inferred← citeshttps://doi.org/10.2174/138620712799361825openalex-snapshot

Computer-Aided Drug Design: Lead Discovery and Optimization

inferred← citeshttps://doi.org/10.2174/156802609789044416openalex-snapshot

Development of Extracellular Signal-Regulated Kinase Inhibitors

inferred← citeshttps://doi.org/10.3329/bjp.v14i1.38871openalex-snapshot

A potential estrogen receptor inhibitor compound 34 induces apoptosis via ROS-independent intrinsic apoptosis in MCF-7 cells

inferred← citeshttps://doi.org/10.3390/ijms13078752openalex-snapshot

Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction

inferred← citeshttps://doi.org/10.4049/jimmunol.1602059openalex-snapshot

Novel Noncatalytic Substrate-Selective p38α-Specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-Inflammatory Activity

inferred← citeshttps://doi.org/10.4155/ebo.13.141openalex-snapshot

Computational approaches for the design of protein–protein interaction inhibitors

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.