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A new test set for validating predictions of protein–ligand interaction
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
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High resolution fast quantitative docking using fourier domain correlation techniques
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Flexible ligand docking: A multistep strategy approach
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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An alternative view of protein fold space
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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SuperStar: A Knowledge-based Approach for Identifying Interaction Sites in Proteins
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Knowledge-based scoring function to predict protein-ligand interactions
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Superstar: improved knowledge-based interaction fields for protein binding sites11Edited by R. Huber
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Superstar: comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions 1 1Edited by R. Huber
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Nonparametric statistics for the behavioral sciences
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Molecular Recognition of Macrocyclic Peptidomimetic Inhibitors by HIV-1 Protease,
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New Approach to Molecular Docking and Its Application to Virtual Screening of Chemical Databases
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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
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Intermolecular Nonbonded Contact Distances in Organic Crystal Structures: Comparison with Distances Expected from van der Waals Radii
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IsoStar: A library of information about nonbonded interactions
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MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
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Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation
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DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
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The CCP4 suite: programs for protein crystallography
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Identifying common metalloprotease inhibitors by protein fold types using Fourier Transform Mass Spectrometry
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Discrimination between the regioisomeric 1,2- and 1,3-diacylglycerophosphocholines by phospholipases
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.08.007openalex-snapshot
Assessing the similarity of ligand binding conformations with the Contact Mode Score
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2011.12.009openalex-snapshot
Prediction of the mode of interaction between monoterpenes and the nitroreductase from Enterobacter cloacae by docking simulation
inferred← citeshttps://doi.org/10.1016/j.cplett.2012.07.016openalex-snapshot
Analysis of surface structures of hydrogen bonding in protein–ligand interactions using the alpha shape model
inferred← citeshttps://doi.org/10.1016/j.ddtec.2004.08.004openalex-snapshot
Scoring functions for protein–ligand interactions: a critical perspective
inferred← citeshttps://doi.org/10.1016/j.drudis.2008.06.006openalex-snapshot
Limitations and lessons in the use of X-ray structural information in drug design
inferred← citeshttps://doi.org/10.1016/j.drudis.2012.06.011openalex-snapshot
Essential considerations for using protein–ligand structures in drug discovery
inferred← citeshttps://doi.org/10.1016/j.ejmech.2006.12.028openalex-snapshot
In-silico drug screening method based on the protein–compound affinity matrix using the factor selection technique
inferred← citeshttps://doi.org/10.1016/j.ejmech.2010.06.024openalex-snapshot
Ligand and structure based pharmacophore modeling to facilitate novel histone deacetylase 8 inhibitor design
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.02.007openalex-snapshot
Pharmacophore-based virtual screening and Bayesian model for the identification of potential human leukotriene A4 hydrolase inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.03.035openalex-snapshot
Potential virtual lead identification in the discovery of renin inhibitors: Application of ligand and structure-based pharmacophore modeling approaches
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.12.006openalex-snapshot
Synthesis and biological activity of novel organoselenium derivatives targeting multiple kinases and capable of inhibiting cancer progression to metastases
inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.05.029openalex-snapshot
The effect of PLC-γ2 inhibitors on the growth of human tumour cells
inferred← citeshttps://doi.org/10.1016/j.ejphar.2018.03.014openalex-snapshot
Diverse signalling of the platelet P2Y1 receptor leads to a dichotomy in platelet function
inferred← citeshttps://doi.org/10.1016/j.ejps.2010.11.010openalex-snapshot
Biarylmethoxy isonipecotanilides as potent and selective inhibitors of blood coagulation factor Xa
inferred← citeshttps://doi.org/10.1016/j.ejps.2016.04.012openalex-snapshot
Identifying GSK-3β kinase inhibitors of Alzheimer's disease: Virtual screening, enzyme, and cell assays
inferred← citeshttps://doi.org/10.1016/j.ejps.2021.106012openalex-snapshot
Inhibition of the RNA-dependent RNA Polymerase of the SARS-CoV-2 by Short Peptide Inhibitors
inferred← citeshttps://doi.org/10.1016/j.febslet.2006.08.037openalex-snapshot
Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors
inferred← citeshttps://doi.org/10.1016/j.freeradbiomed.2020.05.011openalex-snapshot
Lipid aldehyde hydrophobicity affects apo-SOD1 modification and aggregation
inferred← citeshttps://doi.org/10.1016/j.ibmb.2007.09.006openalex-snapshot
Implication of HMGR in homeostasis of sequestered and de novo produced precursors of the iridoid biosynthesis in leaf beetle larvae
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.125367openalex-snapshot
In-silico identification of lysine residue for lysozyme immobilization on dialdehyde cellulose
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.138808openalex-snapshot
Molecular modeling of cellulose tosylate immobilized α-amylases: An in silico case study through MD simulation and refinement
inferred← citeshttps://doi.org/10.1016/j.jinorgbio.2009.12.022openalex-snapshot
QM/MM X-ray refinement of zinc metalloenzymes
inferred← citeshttps://doi.org/10.1016/j.jmb.2006.04.024openalex-snapshot
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
inferred← citeshttps://doi.org/10.1016/j.jmgm.2005.04.004openalex-snapshot
Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2005.06.002openalex-snapshot
Structural model of the Plasmodium CDK, Pfmrk, a novel target for malaria therapeutics
inferred← citeshttps://doi.org/10.1016/j.jmgm.2005.11.006openalex-snapshot
Multiple target screening method for robust and accurate in silico ligand screening
inferred← citeshttps://doi.org/10.1016/j.jmgm.2006.02.010openalex-snapshot
A theory of mode of action of azolylalkylquinolines as DNA binding agents using automated flexible ligand docking
inferred← citeshttps://doi.org/10.1016/j.jmgm.2006.05.001openalex-snapshot
Finding ligands for G protein-coupled receptors based on the protein–compound affinity matrix
inferred← citeshttps://doi.org/10.1016/j.jmgm.2006.08.004openalex-snapshot
High throughput processing of the structural information in the protein data bank
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.04.012openalex-snapshot
Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.07.001openalex-snapshot
Prediction of protein–ligand complex structure by docking software guided by other complex structures
inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.08.003openalex-snapshot
Development of accurate binding affinity predictions of novel renin inhibitors through molecular docking studies
inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.08.002openalex-snapshot
Protein–ligand docking guided by ligand pharmacophore-mapping experiment by NMR
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.03.021openalex-snapshot
Pharmacophore searching: A potential solution for correcting unknown ligands (UNK) labelling errors in Protein Data Bank (PDB’S)
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.09.007openalex-snapshot
Embracing chemical and structural diversity with UCONGA: A universal conformer generation and analysis program
inferred← citeshttps://doi.org/10.1016/j.jphotobiol.2016.11.011openalex-snapshot
Proposed binding mechanism of galbanic acid extracted from Ferula assa–foetida to DNA
inferred← citeshttps://doi.org/10.1016/j.jphysparis.2005.12.084openalex-snapshot
Development and virtual screening of target libraries
inferred← citeshttps://doi.org/10.1016/j.jsps.2020.02.015openalex-snapshot
Anticancer activity of THMPP: Downregulation of PI3K/ S6K1 in breast cancer cell line
inferred← citeshttps://doi.org/10.1016/j.jtbi.2012.10.028openalex-snapshot
A simple iterative method to optimize protein–ligand-binding residue prediction
inferred← citeshttps://doi.org/10.1016/j.molstruc.2022.133741openalex-snapshot
Investigation on crystal structure, spectral FT-IR analysis, DFT and molecular docking studies of a novel complex with the N′-(pyridin-2-ylmethylene)nicotinohydrazide
inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.136924openalex-snapshot
Synthesis, characterization and biological activity of a novel N1, N5-bis[2-hydroxyphenyl]-2-methyl-1,5-diaminopentane Schiff base: Effect of methylene spacers on biological activities
inferred← citeshttps://doi.org/10.1016/j.molstruc.2024.139078openalex-snapshot
Pharmacologically important tetraaza macrocyclic Schiff base complexes of Zn(II), Cu(II) and Co(II): Synthesis, characterization, DFT studies, molecular docking and in vitro anti-bacterial and anti-cancer studies
inferred← citeshttps://doi.org/10.1016/j.phytochem.2011.08.013openalex-snapshot
Lignans as food constituents with estrogen and antiestrogen activity
inferred← citeshttps://doi.org/10.1016/j.ymeth.2008.05.008openalex-snapshot
Modulation of biomolecular interactions with complex-binding small molecules
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.08.001openalex-snapshot
Virtual screening: An in silico tool for interlacing the chemical universe with the proteome
inferred← citeshttps://doi.org/10.1016/s0014-5793(03)00692-6openalex-snapshot
Receptor–drug association studies in the inhibition of the hematin aggregation process of malaria
inferred← citeshttps://doi.org/10.1016/s0303-2647(03)00135-7openalex-snapshot
Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids
inferred← citeshttps://doi.org/10.1016/s0922-3487(03)23004-5openalex-snapshot
Genetic algorithms in molecular modelling: a review
inferred← citeshttps://doi.org/10.1016/s0959-440x(03)00075-7openalex-snapshot
Ligand binding: functional site location, similarity and docking
inferred← citeshttps://doi.org/10.1016/s0969-2126(03)00186-2openalex-snapshot
Pound-Wise but Penny-Foolish
inferred← citeshttps://doi.org/10.1016/s1093-3263(03)00124-4openalex-snapshot
Analysis and optimization of structure-based virtual screening protocols
inferred← citeshttps://doi.org/10.1016/s1093-3263(03)00125-6openalex-snapshot
Analysis and optimization of structure-based virtual screening protocols
inferred← citeshttps://doi.org/10.1016/s1359-6446(05)03484-7openalex-snapshot
Keynote review: Structural biology and drug discovery
inferred← citeshttps://doi.org/10.1016/s1574-1400(06)02010-xopenalex-snapshot
Chapter 10 Cytochrome P450 Enzymes: Computational Approaches to Substrate Prediction
inferred← citeshttps://doi.org/10.1017/cbo9781139021500.015openalex-snapshot
Screening Informatics and Cheminformatics
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00618openalex-snapshot
MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00693openalex-snapshot
LEADS-FRAG: A Benchmark Data Set for Assessment of Fragment Docking Performance
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01358openalex-snapshot
MSLDOCK: Multi-Swarm Optimization for Flexible Ligand Docking and Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00613openalex-snapshot
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00095openalex-snapshot
Rescoring Virtual Screening Results with the MM-PBSA Methods: Beware of Internal Dielectric Constants
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c00228openalex-snapshot
The Good, the Bad, and the Twisted Revisited: An Analysis of Ligand Geometry in Highly Resolved Protein–Ligand X-ray Structures
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b00746openalex-snapshot
Development of N -(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors
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