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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
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Outgoing claims: the papers this work cites, builds on, or argues with.
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inferred← citeshttps://doi.org/10.1002/bit.27618openalex-snapshot
Recent advances in computational methods for biosensor design
inferred← citeshttps://doi.org/10.1002/bit.29044openalex-snapshot
Rational Design and Protein Engineering of {SH2 Domain–≫ Flexible Linker–≫ Self‐Controlling Peptide} Fusion System With Phosphorylation‐Regulated Molecular Switch Functionality
inferred← citeshttps://doi.org/10.1002/bkcs.70207openalex-snapshot
Structural and energetic insights into SARS ‐ CoV ‐2 nucleocapsid protein inhibitors from molecular dynamics and MM ‐ PBSA analyses
inferred← citeshttps://doi.org/10.1002/cbdv.201500513openalex-snapshot
Rational Molecular Design of Potent PLK 1 PBD Domain‐binding Phosphopeptides Using Preferential Amino Acid Building Blocks
inferred← citeshttps://doi.org/10.1002/cbdv.201800159openalex-snapshot
HIV ‐1 Entry Inhibitors: A Review of Experimental and Computational Studies
inferred← citeshttps://doi.org/10.1002/cbdv.201800518openalex-snapshot
Covalent vs. Non‐Covalent Inhibition: Tackling Drug Resistance in EGFR – A Thorough Dynamic Perspective
inferred← citeshttps://doi.org/10.1002/cbdv.202000802openalex-snapshot
Investigating the Mechanistic Inhibitory Discrepancies of Novel Halogen and Alkyl Di‐Substituted Oxadiazole‐Based Dibenzo‐Azepine‐Dione Derivatives on Poly (ADP‐Ribose) Polymerase‐1
inferred← citeshttps://doi.org/10.1002/cbdv.202100204openalex-snapshot
Insight into the Therapeutic Potential of a Bicyclic Hydroxypyridone Compound 2‐[(2,4‐Dichlorophenyl)methyl]‐7‐hydroxy‐1,2,3,4‐tetrahydro‐8H‐pyrido[1,2‐a]pyrazin‐8‐one as COMT Inhibitor in the Treatment of Parkinson's Disease: A Molecular Dynamic Simulation Approach
inferred← citeshttps://doi.org/10.1002/cbdv.202100748openalex-snapshot
Dual‐Inhibition of Human N‐Myristoyltransferase Subtypes Halts Common Cold Pathogenesis: Atomistic Perspectives from the Case of IMP‐1088**
inferred← citeshttps://doi.org/10.1002/cbdv.202200160openalex-snapshot
Molecular Modelling and Atomistic Insights into the Binding Mechanism of MmpL3 Mtb
inferred← citeshttps://doi.org/10.1002/cbdv.202201089openalex-snapshot
Antiproliferative Noscapinoids Bearing an Amidothiadiazole Scaffold as Apoptosis Inducers: Design, Synthesis and Molecular Docking
inferred← citeshttps://doi.org/10.1002/cbdv.202300325openalex-snapshot
Design, Synthesis, Molecular Docking, and Molecular Dynamics Simulation Studies of Novel 3‐Hydroxypyridine‐4‐one Derivatives as Potential Acetylcholinesterase Inhibitors
inferred← citeshttps://doi.org/10.1002/cbdv.202301986openalex-snapshot
Facile and Novel Synthetic Approach, Molecular Docking, Molecular Dynamics, and Drug‐Likeness Evaluation of 9‐Substituted Acridine Derivatives as Dual Anticancer and Antimicrobial Agents
inferred← citeshttps://doi.org/10.1002/cbdv.202403368openalex-snapshot
Computational Evaluation of Phytocompounds From Selective Medicinal Plants as Potential Antidiabetic Agents
inferred← citeshttps://doi.org/10.1002/cbf.3709openalex-snapshot
Computational targeting of allosteric site of MEK1 by quinoline‐based molecules
inferred← citeshttps://doi.org/10.1002/cbic.200600535openalex-snapshot
Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments
inferred← citeshttps://doi.org/10.1002/cbic.201100051openalex-snapshot
A Fast and Precise Approach for Computational Saturation Mutagenesis and its Experimental Validation by Using an Artificial (βα)8‐Barrel Protein
inferred← citeshttps://doi.org/10.1002/cbic.201402003openalex-snapshot
Investigation of Binding‐Site Homology between Mushroom and Bacterial Tyrosinases by Using Aurones as Effectors
inferred← citeshttps://doi.org/10.1002/cbic.201700519openalex-snapshot
Toward a Novel Drug To Target the EGF–EGFR Interaction: Design of Metabolically Stable Bicyclic Peptides
inferred← citeshttps://doi.org/10.1002/cbic.201900051openalex-snapshot
Distinct Dynamic and Conformational Features of Human STING in Response to 2′3′‐cGAMP and c‐di‐GMP
inferred← citeshttps://doi.org/10.1002/cbic.202200533openalex-snapshot
A Chimeric Peptide Inhibits Red Blood Cell Invasion by Plasmodium falciparum with Hundredfold Increased Efficacy**
inferred← citeshttps://doi.org/10.1002/cbic.202300163openalex-snapshot
Biophysical and Computational Approaches to Study Ternary Complexes: A ‘Cooperative Relationship’ to Rationalize Targeted Protein Degradation
inferred← citeshttps://doi.org/10.1002/cbic.202400235openalex-snapshot
Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical Studies
inferred← citeshttps://doi.org/10.1002/cbic.202400555openalex-snapshot
Bridging the Gap in the Structure–Function Paradigm of Enzymatic PET Degradation–Aromatic Residue Driven Balanced Interactions with Catalytic and Anchoring Subsite
inferred← citeshttps://doi.org/10.1002/cbic.202400967openalex-snapshot
Mechanistic Insights into Loop Dynamics in Reshaping the Conformation of YB‐1 Cold Shock Domain
inferred← citeshttps://doi.org/10.1002/chem.200305624openalex-snapshot
Multiple Binding Modes of the Camptothecin Family to DNA Oligomers
inferred← citeshttps://doi.org/10.1002/chem.200800993openalex-snapshot
Design of Protonated Polyazamacrocycles Based on Phenanthroline Motifs for Selective Uptake of Aromatic Carboxylate Anions and Herbicides
inferred← citeshttps://doi.org/10.1002/chem.200902546openalex-snapshot
Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach
inferred← citeshttps://doi.org/10.1002/chem.201102703openalex-snapshot
Probing the Structure of Lysozyme–Carbon‐Nanotube Hybrids with Molecular Dynamics
inferred← citeshttps://doi.org/10.1002/chem.201103467openalex-snapshot
Additional Base‐Pair Formation in DNA Duplexes by a Double‐Headed Nucleotide
inferred← citeshttps://doi.org/10.1002/chem.201301244openalex-snapshot
Conformational Selection in Glycomimetics: Human Galectin‐1 Only Recognizes syn‐Ψ‐Type Conformations of β‐1,3‐Linked Lactose and Its C‐Glycosyl Derivative
inferred← citeshttps://doi.org/10.1002/chem.201301590openalex-snapshot
A Platinum(II) Phenylphenanthroimidazole with an Extended Side‐Chain Exhibits Slow Dissociation from a c‐Kit G‐Quadruplex Motif
inferred← citeshttps://doi.org/10.1002/chem.201405259openalex-snapshot
Specificity of Furanoside–Protein Recognition through Antibody Engineering and Molecular Modeling
inferred← citeshttps://doi.org/10.1002/chem.201503748openalex-snapshot
A Combined Crystallographic and Theoretical Study Explains the Capability of Carboxylic Acids to Adopt Multiple Binding Modes in the Active Site of Carbonic Anhydrases
inferred← citeshttps://doi.org/10.1002/chem.201605430openalex-snapshot
What a Difference a Methyl Group Makes: The Selectivity of Monoamine Oxidase B Towards Histamine and N‐Methylhistamine
inferred← citeshttps://doi.org/10.1002/chem.201901480openalex-snapshot
Computational Design and Study of Artificial Selenoenzyme with Controllable Activity Based on an Allosteric Protein Scaffold
inferred← citeshttps://doi.org/10.1002/chem.202201081openalex-snapshot
Phosphorescence Induction by Host‐Guest Complexation with Cyclodextrins – The Role of Regioisomerism and Affinity
inferred← citeshttps://doi.org/10.1002/chem.71732openalex-snapshot
Targeted Colorectal Cancer Therapy Using Cabozantinib‐Loaded PLGA Nanoparticles: Formulation, Cytotoxicity, and Molecular Docking Analysis
inferred← citeshttps://doi.org/10.1002/chin.200110299openalex-snapshot
ChemInform Abstract: Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferred← citeshttps://doi.org/10.1002/chir.20571openalex-snapshot
Molecular dynamics study on the conformational flexibility and energetics in aqueous solution of methylated β‐cyclodextrins
inferred← citeshttps://doi.org/10.1002/cjoc.201180241openalex-snapshot
Computational Characterization of Binding of Small Molecule Inhibitors to HIV‐1 gp41
inferred← citeshttps://doi.org/10.1002/cmdc.200700087openalex-snapshot
Overcoming the Inadequacies or Limitations of Experimental Structures as Drug Targets by Using Computational Modeling Tools and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1002/cmdc.200700091openalex-snapshot
Homology Modeling of NR2B Modulatory Domain of NMDA Receptor and Analysis of Ifenprodil Binding
inferred← citeshttps://doi.org/10.1002/cmdc.200800186openalex-snapshot
Diazoniapolycyclic Ions Inhibit the Activity of Topoisomerase I and the Growth of Certain Tumor Cell Lines
inferred← citeshttps://doi.org/10.1002/cmdc.201200372openalex-snapshot
Receptor‐Based Virtual Screening and Biological Characterization of Human Apurinic/Apyrimidinic Endonuclease (Ape1) Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201300166openalex-snapshot
Selective and Brain‐Permeable Polo‐like Kinase‐2 (Plk‐2) Inhibitors That Reduce α‐Synuclein Phosphorylation in Rat Brain
inferred← citeshttps://doi.org/10.1002/cmdc.201300176openalex-snapshot
Inhibition of Leishmania infantum Trypanothione Reductase by Azole‐Based Compounds: a Comparative Analysis with Its Physiological Substrate by X‐ray Crystallography
inferred← citeshttps://doi.org/10.1002/cmdc.201300456openalex-snapshot
Computational and Experimental Insight into the Molecular Mechanism of Carboxamide Inhibitors of Succinate‐Ubquinone Oxidoreductase
inferred← citeshttps://doi.org/10.1002/cmdc.201402015openalex-snapshot
Design, Synthesis, and Biological Evaluation of 1,3‐Diarylpropenones as Dual Inhibitors of HIV‐1 Reverse Transcriptase
inferred← citeshttps://doi.org/10.1002/cmdc.201402020openalex-snapshot
DNA Binding Dynamics and Energetics of Cobalt, Nickel, and Copper Metallopeptides
inferred← citeshttps://doi.org/10.1002/cmdc.201402203openalex-snapshot
Atomistic‐Level Portrayal of Drug–DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
inferred← citeshttps://doi.org/10.1002/cmdc.201402394openalex-snapshot
Targeting Promoter G‐Quadruplex DNAs by Indenopyrimidine‐Based Ligands
inferred← citeshttps://doi.org/10.1002/cmdc.201500067openalex-snapshot
Indolo[3,2‐c]quinoline G‐Quadruplex Stabilizers: a Structural Analysis of Binding to the Human Telomeric G‐Quadruplex
inferred← citeshttps://doi.org/10.1002/cmdc.201600015openalex-snapshot
Studies on Cycloheptathiophene‐3‐carboxamide Derivatives as Allosteric HIV‐1 Ribonuclease H Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201600140openalex-snapshot
Cyclic Ketoximes as Estrogen Receptor β Selective Agonists
inferred← citeshttps://doi.org/10.1002/cmdc.201600220openalex-snapshot
Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches
inferred← citeshttps://doi.org/10.1002/cmdc.201600387openalex-snapshot
Design, Synthesis, and Evaluation of Dasatinib–Amino Acid and Dasatinib–Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201800093openalex-snapshot
Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1002/cmdc.201800224openalex-snapshot
Structure‐Based Design of a Monosaccharide Ligand Targeting Galectin‐8
inferred← citeshttps://doi.org/10.1002/cmdc.201800701openalex-snapshot
A Multi‐step Virtual Screening Protocol for the Identification of Novel Non‐acidic Microsomal Prostaglandin E2 Synthase‐1 (mPGES‐1) Inhibitors
inferred← citeshttps://doi.org/10.1002/cmdc.201800779openalex-snapshot
Diamondoid Amino Acid‐Based Peptide Kinase A Inhibitor Analogues
inferred← citeshttps://doi.org/10.1002/cmdc.202000125openalex-snapshot
4‐Fluorobenzylpiperazine‐Containing Derivatives as Efficient Inhibitors of Mushroom Tyrosinase
inferred← citeshttps://doi.org/10.1002/cmdc.202400452openalex-snapshot
Virtual and in Vitro Screening Employing a Repurposing Approach Reveal 13‐cis‐Retinoic Acid is a PTP1B Inhibitor
inferred← citeshttps://doi.org/10.1002/cmdc.202400567openalex-snapshot
Towards New Anti‐Inflammatory Agents: Design, Synthesis and Evaluation of Molecules Targeting XIAP‐BIR2
inferred← citeshttps://doi.org/10.1002/cnm.2914openalex-snapshot
Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1002/cphc.200900132openalex-snapshot
Site‐Dependent Excited‐State Dynamics of a Fluorescent Probe Bound to Avidin and Streptavidin
inferred← citeshttps://doi.org/10.1002/cphc.201000692openalex-snapshot
Stability and Dynamics of Cyclic Diguanylic Acid in Solution
inferred← citeshttps://doi.org/10.1002/cphc.201100339openalex-snapshot
Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free‐Energy Methods
inferred← citeshttps://doi.org/10.1002/cphc.201700337openalex-snapshot
Electrostatics Explains the Position‐Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes
inferred← citeshttps://doi.org/10.1002/cphc.201900903openalex-snapshot
Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2
inferred← citeshttps://doi.org/10.1002/cphc.202000873openalex-snapshot
Cell‐Penetrating Peptides: Correlation between Peptide‐Lipid Interaction and Penetration Efficiency
inferred← citeshttps://doi.org/10.1002/cphc.202200330openalex-snapshot
Microhydration of Phenyl Formate: Gas‐Phase Laser Spectroscopy, Microwave Spectroscopy, and Quantum Chemistry Calculations
inferred← citeshttps://doi.org/10.1002/cphc.202200770openalex-snapshot
A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II
inferred← citeshttps://doi.org/10.1002/cphc.202400412openalex-snapshot
Atomic Insight into the Enzymatic Selectivity of Acetyltransferase for Endogenous Polyamines
inferred← citeshttps://doi.org/10.1002/cplu.201200141openalex-snapshot
Synthesis, Physicochemical Studies, Molecular Dynamics Simulations, and Metal‐Ion‐Dependent Antiproliferative and Antiangiogenic Properties of Cone ICL670‐Substituted Calix[4]arenes
inferred← citeshttps://doi.org/10.1002/cplu.201300199openalex-snapshot
The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design
inferred← citeshttps://doi.org/10.1002/cplu.202000120openalex-snapshot
SQM/COSMO Scoring Function: Reliable Quantum‐Mechanical Tool for Sampling and Ranking in Structure‐Based Drug Design
inferred← citeshttps://doi.org/10.1002/cssc.202102152openalex-snapshot
Production of 10‐Hydroxy‐2‐decenoic Acid from Decanoic Acid via Whole‐Cell Catalysis in Engineered Escherichia coli
inferred← citeshttps://doi.org/10.1002/ddr.20400openalex-snapshot
Molecular simulations for the evaluation of binding free energies in lead optimization
inferred← citeshttps://doi.org/10.1002/ejoc.201200339openalex-snapshot
Modular Solid‐Phase Synthesis of Teroxazoles as a Class of α‐Helix Mimetics
inferred← citeshttps://doi.org/10.1002/ffj.3121openalex-snapshot
Interaction between odorants and proteins involved in the perception of smell: the case of odorant‐binding proteins probed by molecular modelling and biophysical data
inferred← citeshttps://doi.org/10.1002/fsh3.70036openalex-snapshot
Exploring the Multifunctional Agents of Flavonoid‐Rich Beet Leaf Extracts: Insights From Experimental and Computational Studies
inferred← citeshttps://doi.org/10.1002/fsn3.71749openalex-snapshot
Isolation, Purification, Identification, and In Vitro ACE Inhibitory Activity of Tyrosine‐Arginine Dipeptide From Red Millet Huangjiu
inferred← citeshttps://doi.org/10.1002/humu.20379openalex-snapshot
Structural assessment of single amino acid mutations: application to TP53 function
inferred← citeshttps://doi.org/10.1002/iid3.70166openalex-snapshot
Identification and Exploration of Immunity‐Related Genes and Natural Products for Alzheimer's Disease Based on Bioinformatics, Molecular Docking, and Molecular Dynamics
inferred← citeshttps://doi.org/10.1002/ijc.25418openalex-snapshot
Imatinib response in two GIST patients carrying two hitherto functionally uncharacterized PDGFRA mutations: An imaging, biochemical and molecular modeling study
inferred← citeshttps://doi.org/10.1002/ijc.32617openalex-snapshot
Osimertinib confers potent binding affinity to EGFR kinase domain duplication
inferred← citeshttps://doi.org/10.1002/ijch.201400006openalex-snapshot
The Treatment of Solvent in Multiscale Biophysical Modeling
inferred← citeshttps://doi.org/10.1002/ijch.201600127openalex-snapshot
Engineering the Fullerene‐protein Interface by Computational Design: The Sum is More than its Parts
inferred← citeshttps://doi.org/10.1002/jcb.25928openalex-snapshot
Molecular Dynamics Studies on the Enzalutamide Resistance Mechanisms Induced by Androgen Receptor Mutations
inferred← citeshttps://doi.org/10.1002/jcb.26435openalex-snapshot
Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains
inferred← citeshttps://doi.org/10.1002/jcb.26522openalex-snapshot
Biological evaluation and energetic analyses of novel GSK‐3 β inhibitors
inferred← citeshttps://doi.org/10.1002/jcb.26666openalex-snapshot
A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants
inferred← citeshttps://doi.org/10.1002/jcb.27316openalex-snapshot
Exploring the effect of E76K mutation on SHP2 cause gain‐of‐function activity by a molecular dynamics study
inferred← citeshttps://doi.org/10.1002/jcb.28891openalex-snapshot
Halting ionic shuttle to disrupt the synthetic machinery—Structural and molecular insights into the inhibitory roles of Bedaquiline towards Mycobacterium tuberculosis ATP synthase in the treatment of tuberculosis
inferred← citeshttps://doi.org/10.1002/jcb.30109openalex-snapshot
Comparison of potential inhibitors and targeting fat mass and obesity‐associated protein causing diabesity through docking and molecular dynamics strategies
inferred← citeshttps://doi.org/10.1002/jcb.30142openalex-snapshot
Computational decomposition reveals reshaping of the SARS‐CoV‐2–ACE2 interface among viral variants expressing the N501Y mutation
inferred← citeshttps://doi.org/10.1002/jcb.30213openalex-snapshot
Integrative multiomics and in silico analysis revealed the role of ARHGEF1 and its screened antagonist in mild and severe COVID‐19 patients
inferred← citeshttps://doi.org/10.1002/jcb.30493openalex-snapshot
Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all‐atoms molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/jcb.70025openalex-snapshot
“Exploration of Novel Anticancerous Agents Targeting Human Aurora Kinase C”
inferred← citeshttps://doi.org/10.1002/jcb.70058openalex-snapshot
Structure‐Based Identification and Molecular Characterization of CID‐2135609 as a Potent Small Molecule Modulator of HIV‐1 Protease
inferred← citeshttps://doi.org/10.1002/jcc.10099openalex-snapshot
Macrotricyclic quaternary tetraammonium receptors: Halide anion recognition and interfacial activity at an aqueous interface. A molecular dynamics investigation
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