On the public citation graph

Postprocessing of Protein−Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors

0 signed · 72 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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)1096-987x(199604)17:5/6<520::aid-jcc2>3.0.co;2-wopenalex-snapshot
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<553::aid-jcc3>3.0.co;2-topenalex-snapshot
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<587::aid-jcc4>3.0.co;2-qopenalex-snapshot
Merck molecular force field. IV. conformational energies and geometries for MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<616::aid-jcc5>3.0.co;2-xopenalex-snapshot
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199905)20:7<720::aid-jcc7>3.0.co;2-xopenalex-snapshot
MMFF VI. MMFF94s option for energy minimization studies
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199905)20:7<730::aid-jcc8>3.0.co;2-topenalex-snapshot
MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries
inferredcites →https://doi.org/10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-fopenalex-snapshot
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
inferredcites →https://doi.org/10.1002/jcc.10120openalex-snapshot
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
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.20035openalex-snapshot
Development and testing of a general amber force field
inferredcites →https://doi.org/10.1002/jcc.21214openalex-snapshot
Computational analysis of the cathepsin B inhibitors activities through LR‐MMPBSA binding affinity calculation based on docked complex
inferredcites →https://doi.org/10.1002/prot.20223openalex-snapshot
Relative free energy of binding and binding mode calculations of HIV‐1 RT inhibitors based on dock‐MM‐PB/GS
inferredcites →https://doi.org/10.1002/prot.21065openalex-snapshot
Structure modeling, ligand binding, and binding affinity calculation (LR‐MM‐PBSA) of human heparanase for inhibition and drug design
inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
inferredcites →https://doi.org/10.1016/0022-2836(82)90505-8openalex-snapshot
Calculation of the electric potential in the active site cleft due to α-helix dipoles
inferredcites →https://doi.org/10.1016/j.bmcl.2005.01.079openalex-snapshot
Structure–activity relationships for 2-anilino-6-phenylpyrido[2,3-d]pyrimidin-7(8H)-ones as inhibitors of the cellular checkpoint kinase Wee1
inferredcites →https://doi.org/10.1016/j.bmcl.2007.12.046openalex-snapshot
Synthesis and structure–activity relationships of soluble 8-substituted 4-(2-chlorophenyl)-9-hydroxypyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of the Wee1 and Chk1 checkpoint kinases
inferredcites →https://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferredcites →https://doi.org/10.1016/j.ejmech.2007.07.016openalex-snapshot
Synthesis and structure–activity relationships of N-6 substituted analogues of 9-hydroxy-4-phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-diones as inhibitors of Wee1 and Chk1 checkpoint kinases
inferredcites →https://doi.org/10.1016/j.ejmech.2008.09.027openalex-snapshot
Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors
inferredcites →https://doi.org/10.1016/s0022-2836(95)80037-9openalex-snapshot
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
inferredcites →https://doi.org/10.1021/ci0601214openalex-snapshot
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method
inferredcites →https://doi.org/10.1021/j100058a043openalex-snapshot
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
inferredcites →https://doi.org/10.1021/ja0573108openalex-snapshot
In Silico Discovery of β-Secretase Inhibitors
inferredcites →https://doi.org/10.1021/jm000375vopenalex-snapshot
Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids
inferredcites →https://doi.org/10.1021/jm00306a012openalex-snapshot
Potential coenzyme inhibitors. III. Some reactions of substituted nicotinamide and dihydronicotinamide derivatives
inferredcites →https://doi.org/10.1021/jm0309607openalex-snapshot
Prediction of Ligand Binding Affinity and Orientation of Xenoestrogens to the Estrogen Receptor by Molecular Dynamics Simulations and the Linear Interaction Energy Method
inferredcites →https://doi.org/10.1021/jm049726mopenalex-snapshot
Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation
inferredcites →https://doi.org/10.1021/jm050499dopenalex-snapshot
Discovery of Cell-Permeable Non-Peptide Inhibitors of β-Secretase by High-Throughput Docking and Continuum Electrostatics Calculations
inferredcites →https://doi.org/10.1021/jm0512591openalex-snapshot
4-Phenylpyrrolo[3,4-c]carbazole-1,3(2H,6H)-dione Inhibitors of the Checkpoint Kinase Wee1. Structure−Activity Relationships for Chromophore Modification and Phenyl Ring Substitution
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm070654jopenalex-snapshot
Discovery of Kinase Inhibitors by High-Throughput Docking and Scoring Based on a Transferable Linear Interaction Energy Model
inferredcites →https://doi.org/10.1021/jm7012198openalex-snapshot
Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase
inferredcites →https://doi.org/10.1021/jm960684eopenalex-snapshot
Binding Affinities for Sulfonamide Inhibitors with Human Thrombin Using Monte Carlo Simulations with a Linear Response Method
inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1090/s0025-5718-1970-0258249-6openalex-snapshot
A Family of Variable-Metric Methods Derived by Variational Means
inferredcites →https://doi.org/10.1090/s0025-5718-1970-0274029-xopenalex-snapshot
Conditioning of Quasi-Newton Methods for Function Minimization
inferredcites →https://doi.org/10.1093/comjnl/13.3.317openalex-snapshot
A new approach to variable metric algorithms
inferredcites →https://doi.org/10.1093/imamat/6.1.76openalex-snapshot
The Convergence of a Class of Double-rank Minimization Algorithms 1. General Considerations
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
A new method for predicting binding affinity in computer-aided drug design
inferredcites →https://doi.org/10.1371/journal.pntd.0000356openalex-snapshot
Discovery of a Non-Peptidic Inhibitor of West Nile Virus NS3 Protease by High-Throughput Docking
inferredcites →https://doi.org/10.2174/1386207013330661openalex-snapshot
The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies

What points at this work

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

inferred← citeshttps://doi.org/10.1002/jmr.2266openalex-snapshot
Latest developments in molecular docking: 2010–2011 in review
inferred← citeshttps://doi.org/10.1007/s00044-014-1280-xopenalex-snapshot
Molecular modeling of plant metabolites with anti-Onchocerca activity
inferred← citeshttps://doi.org/10.1007/s11030-013-9437-yopenalex-snapshot
Optimizing lactose hydrolysis by computer-guided modification of the catalytic site of a wild-type enzyme
inferred← citeshttps://doi.org/10.1016/j.bpj.2011.11.2003openalex-snapshot
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding using Computational Alanine-Scanning Mutagenesis
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.01.026openalex-snapshot
Structure-based peptide design targeting intrinsically disordered proteins: Novel histone H4 and H2A peptidic inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.06.007openalex-snapshot
Evaluation of potential Myt1 kinase inhibitors by TR-FRET based binding assay
inferred← citeshttps://doi.org/10.1016/j.ejmech.2013.07.022openalex-snapshot
Toward the design of new DNA G-quadruplex ligands through rational analysis of polymorphism and binding data
inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.02.045openalex-snapshot
Docking and binding free energy calculations of sirtuin inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.10.050openalex-snapshot
Computer-aided design, synthesis and biological characterization of novel inhibitors for PKMYT1
inferred← citeshttps://doi.org/10.1016/j.jinorgbio.2019.110875openalex-snapshot
Exploring DNA binding ability of two novel α-N-heterocyclic thiosemicarbazone palladium(II) complexes
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.07.003openalex-snapshot
Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based α-helix mimetic as dual inhibitors of MDM2 and MDMX
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.07.007openalex-snapshot
Hierarchical virtual screening approaches in small molecule drug discovery
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01952openalex-snapshot
Structure-Based Design of Peptidic Inhibitors of the Interaction between CC Chemokine Ligand 5 (CCL5) and Human Neutrophil Peptides 1 (HNP1)
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b03658openalex-snapshot
Protein–Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems
inferred← citeshttps://doi.org/10.1021/bi2008257openalex-snapshot
Probing the Structural and Energetic Basis of Kinesin–Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
inferred← citeshttps://doi.org/10.1021/ci100493jopenalex-snapshot
Molecular Modeling and Molecular Dynamics Simulation Studies of the GSK3β/ATP/Substrate Complex: Understanding the Unique P+4 Primed Phosphorylation Specificity for GSK3β Substrates
inferred← citeshttps://doi.org/10.1021/ci300618eopenalex-snapshot
Identification of Sumoylation Activating Enzyme 1 Inhibitors by Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci400532bopenalex-snapshot
Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR–Ligand Recognition: The Human A2AAdenosine Receptor as a Key Study
inferred← citeshttps://doi.org/10.1021/ci400628qopenalex-snapshot
Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development
inferred← citeshttps://doi.org/10.1021/ci4007326openalex-snapshot
Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors
inferred← citeshttps://doi.org/10.1039/c3mb70449aopenalex-snapshot
Binding of pyrazole-based inhibitors to Mycobacterium tuberculosis pantothenate synthetase: docking and MM-GB(PB)SA analysis
inferred← citeshttps://doi.org/10.1039/c6ra24299eopenalex-snapshot
Nitrogen-doped 3D porous carbons with iron carbide nanoparticles encapsulated in graphitic layers derived from functionalized MOF as an efficient noble-metal-free oxygen reduction electrocatalysts in both acidic and alkaline media
inferred← citeshttps://doi.org/10.1111/cbdd.12868openalex-snapshot
Construction of explicit models to correlate the structure and the inhibitory activity of aldose reductase: Flavonoids and sulfonyl‐pyridazinones as inhibitors
inferred← citeshttps://doi.org/10.1186/1758-2946-4-s1-p42openalex-snapshot
Postprocessing of molecular docking poses using binding free energy calculations
inferred← citeshttps://doi.org/10.12991/jrespharm.1634330openalex-snapshot
In silico design of potential HCV NS5B inhibitors: a comprehensive approach combining combinatorial library generation, ensemble docking, MM-GBSA calculations, QSAR model development, and molecular dynamics
inferred← citeshttps://doi.org/10.2174/138955712800493843openalex-snapshot
Estimation of the Binding Free Energy by Linear Interaction Energy Models
inferred← citeshttps://doi.org/10.29228/jrp.429openalex-snapshot
Fingerprint-based QSAR Model Generation to Identify Structural Determinants of HCV NS5B Inhibition
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch011openalex-snapshot
Recent Advancements in Docking Methodologies
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch033openalex-snapshot
Recent Advancements in Docking Methodologies
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.