On the public citation graph

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

https://doi.org/10.1021/ci3001088
0 signed · 96 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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)1097-0134(1997)1+<215::aid-prot29>3.0.co;2-qopenalex-snapshot
Flexible protein–ligand docking by global energy optimization in internal coordinates
inferredcites →https://doi.org/10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.3.co;2-iopenalex-snapshot
Flexible protein–ligand docking by global energy optimization in internal coordinates
inferredcites →https://doi.org/10.1002/(sici)1099-1352(199905/06)12:3<177::aid-jmr451>3.0.co;2-zopenalex-snapshot
Prediction of the binding energy for small molecules, peptides and proteins
inferredcites →https://doi.org/10.1002/jmr.949openalex-snapshot
Analysis of full and partial agonists binding toβ2‐adrenergic receptor suggests a role of transmembrane helix V in agonist‐specific conformational changes
inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot
Protein–ligand docking: Current status and future challenges
inferredcites →https://doi.org/10.1002/prot.21214openalex-snapshot
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
inferredcites →https://doi.org/10.1002/prot.22507openalex-snapshot
GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A2a receptor complex
inferredcites →https://doi.org/10.1002/prot.340230314openalex-snapshot
Homology modeling by the ICM method
inferredcites →https://doi.org/10.1006/jmbi.1994.1052openalex-snapshot
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
inferredcites →https://doi.org/10.1007/978-1-61779-588-6_8openalex-snapshot
Ligand-Guided Receptor Optimization
inferredcites →https://doi.org/10.1007/s10822-007-9159-2openalex-snapshot
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
inferredcites →https://doi.org/10.1007/s10822-008-9188-5openalex-snapshot
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
inferredcites →https://doi.org/10.1007/s10822-010-9393-xopenalex-snapshot
Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach
inferredcites →https://doi.org/10.1007/s10822-012-9547-0openalex-snapshot
Docking and scoring with ICM: the benchmarking results and strategies for improvement
inferredcites →https://doi.org/10.1007/s11302-007-9058-yopenalex-snapshot
Pyrazolo-triazolo-pyrimidines as adenosine receptor antagonists: Effect of the N-5 bond type on the affinity and selectivity at the four adenosine receptor subtypes
inferredcites →https://doi.org/10.1016/j.bpj.2011.11.2241openalex-snapshot
Pathway and Mechanism of Drug Binding to G-Protein-Coupled Receptors
inferredcites →https://doi.org/10.1016/j.drudis.2009.01.003openalex-snapshot
Managing protein flexibility in docking and its applications
inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
inferredcites →https://doi.org/10.1016/j.neuropharm.2010.07.009openalex-snapshot
Structure based prediction of subtype-selectivity for adenosine receptor antagonists
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1016/s0026-895x(24)23192-8openalex-snapshot
Accommodating Protein Flexibility in Computational Drug Design,
inferredcites →https://doi.org/10.1021/ci200117nopenalex-snapshot
Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening
inferredcites →https://doi.org/10.1021/ci200257bopenalex-snapshot
Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures
inferredcites →https://doi.org/10.1021/ci2005934openalex-snapshot
Potential and Limitations of Ensemble Docking
inferredcites →https://doi.org/10.1021/ci6004993openalex-snapshot
Supervised Consensus Scoring for Docking and Virtual Screening
inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot
Protein−Ligand Docking against Non-Native Protein Conformers
inferredcites →https://doi.org/10.1021/ci8003732openalex-snapshot
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
inferredcites →https://doi.org/10.1021/ci9003943openalex-snapshot
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
inferredcites →https://doi.org/10.1021/ci900407copenalex-snapshot
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
inferredcites →https://doi.org/10.1021/j100194a068openalex-snapshot
Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
inferredcites →https://doi.org/10.1021/ja042260copenalex-snapshot
Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
inferredcites →https://doi.org/10.1021/ja0709728openalex-snapshot
Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/ja202726yopenalex-snapshot
How Does a Drug Molecule Find Its Target Binding Site?
inferredcites →https://doi.org/10.1021/jm048972vopenalex-snapshot
Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm070759mopenalex-snapshot
Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening
inferredcites →https://doi.org/10.1021/jm8009958openalex-snapshot
Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking
inferredcites →https://doi.org/10.1021/jm801005mopenalex-snapshot
Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking
inferredcites →https://doi.org/10.1021/jm901647popenalex-snapshot
Structure-Based Discovery of Novel Chemotypes for Adenosine A2AReceptor Antagonists
inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot
Implications of protein flexibility for drug discovery
inferredcites →https://doi.org/10.1038/nrd2877openalex-snapshot
Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
inferredcites →https://doi.org/10.1073/pnas.0408930102openalex-snapshot
Molecular dynamics and protein function
inferredcites →https://doi.org/10.1073/pnas.0609752104openalex-snapshot
Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs
inferredcites →https://doi.org/10.1073/pnas.1104614108openalex-snapshot
Pathway and mechanism of drug binding to G-protein-coupled receptors
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1093/bioinformatics/btq504openalex-snapshot
SimiCon: a web tool for protein–ligand model comparison through calculation of equivalent atomic contacts
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1093/nar/gkr825openalex-snapshot
Pocketome: an encyclopedia of small-molecule binding sites in 4D
inferredcites →https://doi.org/10.1186/1471-2105-12-s1-s35openalex-snapshot
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
inferredcites →https://doi.org/10.2174/1381612033454595openalex-snapshot
Conformational Flexibility Models for the Receptor in Structure Based Drug Design
inferredcites →https://doi.org/10.2174/138920306778559368openalex-snapshot
Structure Selection for Protein Kinase Docking and Virtual Screening:Homology Models or Crystal Structures?

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118681121.ch15openalex-snapshot
Computational Structural Biology for Drug Discovery
inferred← citeshttps://doi.org/10.1002/9783527677016.ch3openalex-snapshot
The Human Pocketome
inferred← citeshttps://doi.org/10.1002/cmdc.201500086openalex-snapshot
Protein Flexibility in Drug Discovery: From Theory to Computation
inferred← citeshttps://doi.org/10.1002/jcc.23905openalex-snapshot
DOCK 6: Impact of new features and current docking performance
inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
inferred← citeshttps://doi.org/10.1002/minf.201500080openalex-snapshot
In Silico Investigation of the Neurotensin Receptor 1 Binding Site: Overlapping Binding Modes for Small Molecule Antagonists and the Endogenous Peptide Agonist
inferred← citeshttps://doi.org/10.1007/978-1-4939-2858-3_2openalex-snapshot
Homology Modeling and Docking Evaluation of Human Muscarinic Acetylcholine Receptors
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_15openalex-snapshot
Computational Modeling of Drugs for Alzheimer’s Disease: Design of Serotonin 5-HT6 Antagonists
inferred← citeshttps://doi.org/10.1007/s10822-017-0058-xopenalex-snapshot
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00027-8openalex-snapshot
Molecular Docking for Natural Product Investigations: Pitfalls and Ways to Overcome Them
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00006-6openalex-snapshot
Modeling protein flexibility in molecular docking
inferred← citeshttps://doi.org/10.1016/j.drudis.2013.10.027openalex-snapshot
Modelling three-dimensional protein structures for applications in drug design
inferred← citeshttps://doi.org/10.1016/j.tips.2014.04.004openalex-snapshot
Modeling G protein-coupled receptors in complex with biased agonists
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00263openalex-snapshot
From Homology Models to a Set of Predictive Binding Pockets–a 5-HT1A Receptor Case Study
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00749openalex-snapshot
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00125openalex-snapshot
Modeling Binding with Large Conformational Changes: Key Points in Ensemble-Docking Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00399openalex-snapshot
Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00314openalex-snapshot
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00109openalex-snapshot
Structure-Based Discovery of New Antagonist and Biased Agonist Chemotypes for the Kappa Opioid Receptor
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.2c00160openalex-snapshot
Optimization of First-in-Class Dual-Acting FFAR1/FFAR4 Allosteric Modulators with Novel Mode of Action
inferred← citeshttps://doi.org/10.1021/bi500374topenalex-snapshot
Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/ci3004557openalex-snapshot
Multiple Structures for Virtual Ligand Screening: Defining Binding Site Properties-Based Criteria to Optimize the Selection of the Query
inferred← citeshttps://doi.org/10.1021/ci400203fopenalex-snapshot
Identification of a New Class of FtsZ Inhibitors by Structure-Based Design and in Vitro Screening
inferred← citeshttps://doi.org/10.1021/ci400729jopenalex-snapshot
Ensemble-Based Docking Using Biased Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/ci400742sopenalex-snapshot
Identification of Novel Serotonin Transporter Compounds by Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci500742bopenalex-snapshot
Structure-Based Predictions of Activity Cliffs
inferred← citeshttps://doi.org/10.1038/nchem.1954openalex-snapshot
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery
inferred← citeshttps://doi.org/10.1038/nchembio.1837openalex-snapshot
SMN2 splice modulators enhance U1–pre-mRNA association and rescue SMA mice
inferred← citeshttps://doi.org/10.1038/s41598-018-28263-7openalex-snapshot
Structure-Activity Investigations and Optimisations of Non-metabolite Agonists for the Succinate Receptor 1
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv486openalex-snapshot
Integrated structure- and ligand-basedin silicoapproach to predict inhibition of cytochrome P450 2D6
inferred← citeshttps://doi.org/10.1093/toxsci/kfu114openalex-snapshot
In Silico Identification and Pharmacological Evaluation of Novel Endocrine Disrupting Chemicals That Act via the Ligand-Binding Domain of the Estrogen Receptor α
inferred← citeshttps://doi.org/10.1101/039446openalex-snapshot
Best Practices in Docking and Activity Prediction
inferred← citeshttps://doi.org/10.1111/bph.13452openalex-snapshot
Identifying ligands at orphan GPCRs: current status using structure‐based approaches
inferred← citeshttps://doi.org/10.1124/mol.113.088682openalex-snapshot
The Second Extracellular Loop of the Adenosine A1 Receptor Mediates Activity of Allosteric Enhancers
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005819openalex-snapshot
Improving virtual screening of G protein-coupled receptors via ligand-directed modeling
inferred← citeshttps://doi.org/10.1517/17460441.2015.1094458openalex-snapshot
Understanding the challenges of protein flexibility in drug design
inferred← citeshttps://doi.org/10.18130/v3zb9vopenalex-snapshot
Molecular Mechanisms of Adenosine A1 Receptor Allosteric Enhancers
inferred← citeshttps://doi.org/10.2174/156802612804547335openalex-snapshot
Compound Activity Prediction Using Models of Binding Pockets or Ligand Properties in 3D
inferred← citeshttps://doi.org/10.2174/1568026614666140929153812openalex-snapshot
Recent Advances in Computer-Aided Drug Design as Applied to Anti-Influenza Drug Discovery
inferred← citeshttps://doi.org/10.2174/1568026619666190816101948openalex-snapshot
Virtual Screening Techniques in Drug Discovery: Review and Recent Applications
inferred← citeshttps://doi.org/10.3390/ph5121332openalex-snapshot
Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Docking
inferred← citeshttps://doi.org/10.4155/fmc.15.150openalex-snapshot
Sampling of Conformational Ensemble for Virtual Screening Using Molecular Dynamics Simulations and Normal Mode Analysis
inferred← citeshttps://doi.org/10.6092/unibo/amsdottorato/6330openalex-snapshot
Computational strategies to include protein flexibility in Ligand Docking and Virtual Screening
inferred← citeshttps://doi.org/10.70675/de51bc89z33fez456fz9467z959329cc603bopenalex-snapshot
Optimisation de méthodes de criblage virtuel et synthèse de molécules à visée thérapeutique pour le traitement des maladies auto-immunes.
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.