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gCOMBINE: A graphical user interface to perform structure‐based comparative binding energy (COMBINE) analysis on a set of ligand‐receptor complexes

https://doi.org/10.1002/prot.22543
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.1161openalex-snapshot
Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
inferredcites →https://doi.org/10.1002/prot.21321openalex-snapshot
COMBINE analysis of the specificity of binding of Ras proteins to their effectors
inferredcites →https://doi.org/10.1007/0-306-46857-3_2openalex-snapshot
Comparative Binding Energy Analysis
inferredcites →https://doi.org/10.1016/b978-0-12-103950-9.50017-4openalex-snapshot
Path Models with Latent Variables: The NIPALS Approach
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/j.jmb.2004.09.063openalex-snapshot
Comparative Structural and Energetic Analysis of WW Domain–Peptide Interactions
inferredcites →https://doi.org/10.1016/j.sbi.2006.02.003openalex-snapshot
Comparative modeling for protein structure prediction
inferredcites →https://doi.org/10.1016/s1093-3263(98)00007-2openalex-snapshot
Simulation of alternative binding modes in a structure-based QSAR study of HIV-1 protease inhibitors
inferredcites →https://doi.org/10.1021/bi010464popenalex-snapshot
Comparative Binding Energy Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter autotrophicus GJ10
inferredcites →https://doi.org/10.1021/cr0102009openalex-snapshot
Chem-Bioinformatics: Comparative QSAR at the Interface between Chemistry and Biology
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
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/ja038893topenalex-snapshot
Chemometrical Identification of Mutations in HIV-1 Reverse Transcriptase Conferring Resistance or Enhanced Sensitivity to Arylsulfonylbenzonitriles
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/jm00014a020openalex-snapshot
Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis
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/jm001070jopenalex-snapshot
Comparative Binding Energy (COMBINE) Analysis of Influenza Neuraminidase−Inhibitor Complexes
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/jm020900lopenalex-snapshot
Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics
inferredcites →https://doi.org/10.1021/jm030137aopenalex-snapshot
Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors
inferredcites →https://doi.org/10.1021/jm049695vopenalex-snapshot
A Docking Score Function for Estimating Ligand−Protein Interactions: Application to Acetylcholinesterase Inhibition
inferredcites →https://doi.org/10.1021/jm049877popenalex-snapshot
Modulation of Binding Strength in Several Classes of Active Site Inhibitors of Acetylcholinesterase Studied by Comparative Binding Energy Analysis
inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot
A Critical Assessment of Docking Programs and Scoring Functions
inferredcites →https://doi.org/10.1021/jm060350hopenalex-snapshot
Comparative Binding Energy Analysis Considering Multiple Receptors: A Step toward 3D-QSAR Models for Multiple Targets
inferredcites →https://doi.org/10.1021/jm970535bopenalex-snapshot
Comparative Binding Energy Analysis of HIV-1 Protease Inhibitors: Incorporation of Solvent Effects and Validation as a Powerful Tool in Receptor-Based Drug Design
inferredcites →https://doi.org/10.1021/jm9911175openalex-snapshot
Nuclear Receptor−DNA Binding Specificity: A COMBINE and Free−Wilson QSAR Analysis
inferredcites →https://doi.org/10.1023/a:1008164621650openalex-snapshot
3D-QSAR methods on the basis of ligand–receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands
inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot
Virtual screening of chemical libraries
inferredcites →https://doi.org/10.1093/protein/4.8.903openalex-snapshot
Electrostatic effects in proteins: comparison of dielectric and charge models
inferredcites →https://doi.org/10.1124/mol.106.026427openalex-snapshot
Broad Specificity of Mammalian Adenylyl Cyclase for Interaction with 2′,3′-Substituted Purine- and Pyrimidine Nucleotide Inhibitors
inferredcites →https://doi.org/10.1126/science.7761829openalex-snapshot
Classical Electrostatics in Biology and Chemistry
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/10.1289/ehp.5758openalex-snapshot
Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs.
inferredcites →https://doi.org/10.2174/092986707781058814openalex-snapshot
Whither Combine? New Opportunities for Receptor-Based QSAR
inferredcites →https://doi.org/10.2174/1386207013330742openalex-snapshot
Comparative Binding Energy (COMBINE) Analysis of Human Neutrophil Elastase Inhibition by Pyridone-containing Trifluoromethylketones

What points at this work

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

inferred← citeshttps://doi.org/10.1002/bip.22773openalex-snapshot
Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza‐decaline scaffold
inferred← citeshttps://doi.org/10.1002/cmdc.201200065openalex-snapshot
Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β‐Tubulin
inferred← citeshttps://doi.org/10.1002/cmdc.201300013openalex-snapshot
Comparative Binding Energy (COMBINE) Analysis for Understanding the Binding Determinants of Type II Dehydroquinase Inhibitors
inferred← citeshttps://doi.org/10.1002/jcc.24502openalex-snapshot
Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work
inferred← citeshttps://doi.org/10.1002/jcc.26779openalex-snapshot
Improving ligand‐ranking of AutoDock Vina by changing the empirical parameters
inferred← citeshttps://doi.org/10.1002/smo.20230012openalex-snapshot
Machine learning methods for developments of binding kinetic models in predicting protein‐ligand dissociation rate constants
inferred← citeshttps://doi.org/10.1007/978-1-0716-1209-5_10openalex-snapshot
A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time
inferred← citeshttps://doi.org/10.1007/978-3-319-40259-8_4openalex-snapshot
ARDock: A Web-AR Based Real-Time Tangible Edugame for Molecular Docking
inferred← citeshttps://doi.org/10.1007/s10822-018-0181-3openalex-snapshot
Active learning strategies with COMBINE analysis: new tricks for an old dog
inferred← citeshttps://doi.org/10.1016/b978-0-12-801505-6.00010-7openalex-snapshot
Other Related Techniques
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00639openalex-snapshot
Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.8b00397openalex-snapshot
Prediction of Drug–Target Binding Kinetics by Comparative Binding Energy Analysis
inferred← citeshttps://doi.org/10.1021/acsomega.8b03258openalex-snapshot
Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method
inferred← citeshttps://doi.org/10.1021/cb400673hopenalex-snapshot
Molecular Recognition of Epothilones by Microtubules and Tubulin Dimers Revealed by Biochemical and NMR Approaches
inferred← citeshttps://doi.org/10.1021/ci300160yopenalex-snapshot
Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction
inferred← citeshttps://doi.org/10.1039/9781849735377-00244openalex-snapshot
COMparative BINding Energy (COMBINE) Analysis as a Structure-Based 3D-QSAR Method
inferred← citeshttps://doi.org/10.1039/c3ob40407bopenalex-snapshot
A structure-based design of new C2- and C13-substituted taxanes: tubulin binding affinities and extended quantitative structure–activity relationships using comparative binding energy (COMBINE) analysis
inferred← citeshttps://doi.org/10.1039/c9ra09583gopenalex-snapshot
Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach
inferred← citeshttps://doi.org/10.1039/d2cp04476eopenalex-snapshot
Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches
inferred← citeshttps://doi.org/10.1186/1472-6807-12-21openalex-snapshot
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)
inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-bhb1jopenalex-snapshot
Improving the Accuracy of AutoDock Vina by Changing the Empirical Parameters
inferred← citeshttps://doi.org/10.26434/chemrxiv.14208446openalex-snapshot
Prediction of Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis
inferred← citeshttps://doi.org/10.4155/fmc.12.149openalex-snapshot
Molecular Simulations Of Drug–Receptor Complexes In Anticancer Research
inferred← citeshttps://doi.org/10.70675/2b288725z2446z48c5z833ezf53915cd324bopenalex-snapshot
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