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FireDock: Fast interaction refinement in molecular docking

https://doi.org/10.1002/prot.21495
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000501)39:2<178::aid-prot8>3.0.co;2-6openalex-snapshot
Protein docking using spherical polar Fourier correlations
inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000601)39:4<372::aid-prot100>3.0.co;2-qopenalex-snapshot
BiGGER: A new (soft) docking algorithm for predicting protein interactions
inferredcites →https://doi.org/10.1002/(sici)1097-0282(199908)50:2<111::aid-bip1>3.0.co;2-nopenalex-snapshot
Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/pro.5560060807openalex-snapshot
Bayesian statistical analysis of protein side‐chain rotamer preferences
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot
Successful discrimination of protein interactions
inferredcites →https://doi.org/10.1002/prot.10460openalex-snapshot
RDOCK: Refinement of rigid‐body protein docking predictions
inferredcites →https://doi.org/10.1002/prot.20417openalex-snapshot
Cation–π interactions in protein–protein interfaces
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.340140208openalex-snapshot
Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology
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/10.1006/jmbi.1994.1366openalex-snapshot
Application of a Self-consistent Mean Field Theory to Predict Protein Side-chains Conformation and Estimate Their Conformational Entropy
inferredcites →https://doi.org/10.1006/jmbi.1996.0859openalex-snapshot
Determination of atomic desolvation energies from the structures of crystallized proteins
inferredcites →https://doi.org/10.1006/jmbi.1997.1519openalex-snapshot
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
inferredcites →https://doi.org/10.1006/jmbi.1998.2401openalex-snapshot
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/11415770_32openalex-snapshot
Rapid Protein Side-Chain Packing via Tree Decomposition
inferredcites →https://doi.org/10.1007/3-540-44696-6_10openalex-snapshot
Side Chain-Positioning as an Integer Programming Problem
inferredcites →https://doi.org/10.1007/3-540-45784-4_14openalex-snapshot
Efficient Unbound Docking of Rigid Molecules
inferredcites →https://doi.org/10.1007/bf02579150openalex-snapshot
A new polynomial-time algorithm for linear programming
inferredcites →https://doi.org/10.1016/0022-2836(91)90550-popenalex-snapshot
Prediction of protein side-chain conformation by packing optimization
inferredcites →https://doi.org/10.1016/0041-5553(80)90061-0openalex-snapshot
Polynomial algorithms in linear programming
inferredcites →https://doi.org/10.1016/j.jmb.2003.10.069openalex-snapshot
Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes
inferredcites →https://doi.org/10.1016/j.jmb.2004.07.038openalex-snapshot
Analysis of Anisotropic Side-chain Packing in Proteins and Application to High-resolution Structure Prediction
inferredcites →https://doi.org/10.1016/j.jmb.2004.09.051openalex-snapshot
Protein–Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking
inferredcites →https://doi.org/10.1016/j.jmb.2005.01.058openalex-snapshot
The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking
inferredcites →https://doi.org/10.1016/s0022-2836(03)00670-3openalex-snapshot
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0022-2836(95)80063-8openalex-snapshot
A geometry-based suite of moleculardocking processes
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1038/356539a0openalex-snapshot
The dead-end elimination theorem and its use in protein side-chain positioning
inferredcites →https://doi.org/10.1063/1.1699114openalex-snapshot
Equation of State Calculations by Fast Computing Machines
inferredcites →https://doi.org/10.1063/1.472061openalex-snapshot
Simulation of activation free energies in molecular systems
inferredcites →https://doi.org/10.1073/pnas.0401942101openalex-snapshot
Anchor residues in protein–protein interactions
inferredcites →https://doi.org/10.1073/pnas.202485799openalex-snapshot
A simple physical model for binding energy hot spots in protein–protein complexes
inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1080/00401706.1999.10485951openalex-snapshot
Statistical Learning Theory
inferredcites →https://doi.org/10.1080/07391102.1991.10507882openalex-snapshot
A New Approach to the Rapid Determination of Protein Side Chain Conformations
inferredcites →https://doi.org/10.1089/106652702760277336openalex-snapshot
A Combinatorial Approach to Protein Docking with Flexible Side Chains
inferredcites →https://doi.org/10.1093/bioinformatics/16.9.815openalex-snapshot
BALL—rapid software prototyping in computational molecular biology
inferredcites →https://doi.org/10.1093/bioinformatics/btg371openalex-snapshot
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
inferredcites →https://doi.org/10.1093/bioinformatics/bti144openalex-snapshot
Solving and analyzing side-chain positioning problems using linear and integer programming
inferredcites →https://doi.org/10.1093/bioinformatics/bti763openalex-snapshot
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
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/15.10.779openalex-snapshot
Protein Design is NP-hard
inferredcites →https://doi.org/10.1093/protein/8.4.363openalex-snapshot
Side-chain prediction by neural networks and simulated annealing optimization
inferredcites →https://doi.org/10.1109/ccv.1988.589995openalex-snapshot
Geometric Hashing: A General And Efficient Model-based Recognition Scheme
inferredcites →https://doi.org/10.1110/ps.0239303openalex-snapshot
Protein–protein docking with a reduced protein model accounting for side‐chain flexibility
inferredcites →https://doi.org/10.1110/ps.03154503openalex-snapshot
A graph‐theory algorithm for rapid protein side‐chain prediction
inferredcites →https://doi.org/10.1110/ps.041222905openalex-snapshot
Improved side‐chain modeling for protein–protein docking
inferredcites →https://doi.org/10.1142/s0219720005000904openalex-snapshot
PROTEIN SIDE-CHAIN PACKING PROBLEM: A MAXIMUM EDGE-WEIGHT CLIQUE ALGORITHMIC APPROACH
inferredcites →https://doi.org/10.1515/9781400884179openalex-snapshot
Linear Programming and Extensions

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inferred← citeshttps://doi.org/10.1002/ijch.201200095openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcb.29835openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21394openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21479openalex-snapshot
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Initiation of Apoptotic Pathway by the Cell-Free Supernatant Synthesized from Weissella cibaria Through In-Silico and In-Vitro Methods
inferred← citeshttps://doi.org/10.1007/s12026-022-09351-3openalex-snapshot
In silico design and evaluation of a novel mRNA vaccine against BK virus: a reverse vaccinology approach
inferred← citeshttps://doi.org/10.1007/s12033-022-00612-yopenalex-snapshot
Molecular Cloning, Expression, Sequence Characterization and Structural Insight of Bubalus bubalis Growth Hormone-Receptor
inferred← citeshttps://doi.org/10.1007/s12033-023-00763-6openalex-snapshot
Trypanosoma cruzi Tc24 Antigen Expressed and Orally Delivered by Schizochytrium sp. Microalga is Immunogenic in Mice
inferred← citeshttps://doi.org/10.1007/s12668-019-00707-yopenalex-snapshot
Interaction of Isatin with Cytochrome P450 Isoenzymes: Investigation by Means of Spectral and Electrochemical Methods The role of Isatin in Cytochromes P450 Ligand-Protein Binding Events
inferred← citeshttps://doi.org/10.1007/s13205-013-0146-0openalex-snapshot
Identification of potential inhibitor targeting enoyl-acyl carrier protein reductase (InhA) in Mycobacterium tuberculosis: a computational approach
inferred← citeshttps://doi.org/10.1007/s13205-015-0339-9openalex-snapshot
Molecular dynamic simulations of Escherichia coli l-asparaginase to illuminate its role in deamination of asparagine and glutamine residues
inferred← citeshttps://doi.org/10.1007/s13205-016-0422-xopenalex-snapshot
Exploration of the binding modes of l-asparaginase complexed with its amino acid substrates by molecular docking, dynamics and simulation
inferred← citeshttps://doi.org/10.1007/s13337-019-00521-wopenalex-snapshot
In silico analyses of molecular interactions between groundnut bud necrosis virus and its vector, Thrips palmi
inferred← citeshttps://doi.org/10.1007/s13721-020-00276-1openalex-snapshot
Estimation of drug-likeness properties of GC–MS separated bioactive compounds in rare medicinal Pleione maculata using molecular docking technique and SwissADME in silico tools
inferred← citeshttps://doi.org/10.1007/s13721-023-00416-3openalex-snapshot
A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae
inferred← citeshttps://doi.org/10.1007/s44371-024-00037-3openalex-snapshot
6-hydroxy-3-succinoylsemialdehyde-pyridine as a potential inhibitor of schizophrenia-associated enzyme
inferred← citeshttps://doi.org/10.1016/b978-0-12-801238-3.11315-7openalex-snapshot
Recent Progresses of Computational Analysis of RNA-Protein Interactions
inferred← citeshttps://doi.org/10.1016/b978-0-12-818593-3.00010-5openalex-snapshot
Prospects of omics technologies and bioinformatics approaches in food science
inferred← citeshttps://doi.org/10.1016/b978-0-12-824369-5.00006-3openalex-snapshot
Food and human health: An outlook of the journey of food from hunger satisfaction to health-promoting agent
inferred← citeshttps://doi.org/10.1016/b978-0-443-15457-7.00001-0openalex-snapshot
Deciphering the scope of in silico screening of novel natural lead molecules against putative molecular targets of multidrug-resistant bacterial pathogens
inferred← citeshttps://doi.org/10.1016/b978-8-1312-2297-3.50007-2openalex-snapshot
Protein Interactions
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2017.06.003openalex-snapshot
Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems
inferred← citeshttps://doi.org/10.1016/bs.apcsb.2024.10.011openalex-snapshot
Navigating the landscape: A comprehensive overview of computational approaches in therapeutic antibody design and analysis
inferred← citeshttps://doi.org/10.1016/j.abb.2009.12.017openalex-snapshot
The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation
inferred← citeshttps://doi.org/10.1016/j.abb.2018.05.020openalex-snapshot
Interactive structural analysis of βTrCP1 and PER2 phosphoswitch binding through dynamics simulation assay
inferred← citeshttps://doi.org/10.1016/j.abb.2018.06.004openalex-snapshot
Designing a new multifunctional peptide for metal chelation and Aβ inhibition
inferred← citeshttps://doi.org/10.1016/j.abb.2019.06.003openalex-snapshot
Structural studies of Staphylococcus aureus Sortase inhibiton via Conus venom peptides
inferred← citeshttps://doi.org/10.1016/j.afres.2025.101291openalex-snapshot
AI-driven bioactive peptide discovery of next-generation metabolic biotherapeutics
inferred← citeshttps://doi.org/10.1016/j.atherosclerosis.2023.117436openalex-snapshot
Novel role of peptidoglycan recognition protein 2 in activating NOD2-NFκB inflammatory axis in coronary artery disease
inferred← citeshttps://doi.org/10.1016/j.bbagen.2019.04.015openalex-snapshot
Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management
inferred← citeshttps://doi.org/10.1016/j.bbrc.2013.02.037openalex-snapshot
Heme oxygenase-2/adiponectin protein–protein interaction in metabolic syndrome
inferred← citeshttps://doi.org/10.1016/j.bbrc.2017.08.037openalex-snapshot
Identification of novel direct protein-protein interactions by irradiating living cells with femtosecond UV laser pulses
inferred← citeshttps://doi.org/10.1016/j.bbrc.2025.151623openalex-snapshot
Main methods and tools for peptide development based on protein-protein interactions (PPIs)
inferred← citeshttps://doi.org/10.1016/j.bcp.2008.08.018openalex-snapshot
A selective blocker of Kv1.2 and Kv1.3 potassium channels from the venom of the scorpion Centruroides suffusus suffusus
inferred← citeshttps://doi.org/10.1016/j.biocel.2009.11.002openalex-snapshot
Microcin J25 triggers cytochrome c release through irreversible damage of mitochondrial proteins and lipids
inferred← citeshttps://doi.org/10.1016/j.biochi.2015.07.011openalex-snapshot
α-synuclein dimer structures found from computational simulations
inferred← citeshttps://doi.org/10.1016/j.biochi.2019.02.007openalex-snapshot
Microcin J25 inhibits ubiquinol oxidase activity of purified cytochrome bd-I from Escherichia coli
inferred← citeshttps://doi.org/10.1016/j.biochi.2020.11.004openalex-snapshot
Molecular docking simulation reveals ACE2 polymorphisms that may increase the affinity of ACE2 with the SARS-CoV-2 Spike protein
inferred← citeshttps://doi.org/10.1016/j.biopha.2018.09.166openalex-snapshot
ATRA reduces inflammation and improves alveolar epithelium regeneration in emphysematous rat lung
inferred← citeshttps://doi.org/10.1016/j.biotechadv.2024.108437openalex-snapshot
Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights.
inferred← citeshttps://doi.org/10.1016/j.bmcl.2013.12.119openalex-snapshot
Predicting the molecular interactions of CRIP1a–cannabinoid 1 receptor with integrated molecular modeling approaches
inferred← citeshttps://doi.org/10.1016/j.bpc.2018.07.002openalex-snapshot
Antagonistic role of Klotho-derived peptides dynamics in the pancreatic cancer treatment through obstructing WNT-1 and Frizzled binding
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.11.3519openalex-snapshot
3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling
inferred← citeshttps://doi.org/10.1016/j.btre.2021.e00615openalex-snapshot
Selenium nanoparticles: Synthesis, in-vitro cytotoxicity, antioxidant activity and interaction studies with ct-DNA and HSA, HHb and Cyt c serum proteins
inferred← citeshttps://doi.org/10.1016/j.carbon.2019.02.043openalex-snapshot
Identification and preparation of stable water dispersions of protein - Carbon nanotube hybrids and efficient design of new functional materials
inferred← citeshttps://doi.org/10.1016/j.cell.2022.02.012openalex-snapshot
Tumor-reactive antibodies evolve from non-binding and autoreactive precursors
inferred← citeshttps://doi.org/10.1016/j.chembiol.2008.09.010openalex-snapshot
Proposed Arrangement of Proteins Forming a Bacterial Type II Polyketide Synthase
inferred← citeshttps://doi.org/10.1016/j.colsurfb.2013.07.018openalex-snapshot
Diameter-selective dispersion of carbon nanotubes by β-lactoglobulin whey protein
inferred← citeshttps://doi.org/10.1016/j.colsurfb.2018.11.032openalex-snapshot
Proline functionalized gold nanoparticles modulates lysozyme fibrillation
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2016.07.005openalex-snapshot
In-silico structural analysis of E509K mutation in LARGE and T192M mutation in Alpha Dystroglycan in the inhibition of glycosylation of Alpha Dystroglycan by LARGE
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2021.107487openalex-snapshot
Discovery of new inhibitor for the protein arginine deiminase type 4 (PAD4) by rational design of α-enolase-derived peptides
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2022.107754openalex-snapshot
Exploiting reverse vaccinology approach for the design of a multiepitope subunit vaccine against the major SARS-CoV-2 variants
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2022.107797openalex-snapshot
Integrated in silico and experimental discovery of trimeric peptide ligands targeting Butyrylcholinesterase
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2023.107819openalex-snapshot
Replica-exchange optimization of antibody fragments
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104701openalex-snapshot
Chlamydia trachomatis core genome data mining for promising novel drug targets and chimeric vaccine candidates identification
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104705openalex-snapshot
Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104759openalex-snapshot
Computational screening of 645 antiviral peptides against the receptor-binding domain of the spike protein in SARS-CoV-2
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.105660openalex-snapshot
E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.106128openalex-snapshot
Designing a vaccine-based therapy against Epstein-Barr virus-associated tumors using immunoinformatics approach
inferred← citeshttps://doi.org/10.1016/j.cpc.2020.107716openalex-snapshot
PARCE: Protocol for Amino acid Refinement through Computational Evolution
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.01.012openalex-snapshot
A stepwise docking molecular dynamics approach for simulating antibody recognition with substantial conformational changes
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.08.035openalex-snapshot
Computational design and characterization of a multiepitope vaccine against carbapenemase-producing Klebsiella pneumoniae strains, derived from antigens identified through reverse vaccinology
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.02.031openalex-snapshot
Connection between MHC class II binding and aggregation propensity: The antigenic peptide 10 of Paracoccidioides brasiliensis as a benchmark study
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.04.008openalex-snapshot
The CDR3 region as the major driver of TREM-1 interaction with its ligands, an in silico characterization
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.12.018openalex-snapshot
Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength
inferred← citeshttps://doi.org/10.1016/j.cyto.2014.05.013openalex-snapshot
The critical role of macrophage migration inhibitory factor in insulin activity
inferred← citeshttps://doi.org/10.1016/j.drudis.2014.02.005openalex-snapshot
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
inferred← citeshttps://doi.org/10.1016/j.drudis.2015.03.007openalex-snapshot
Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking
inferred← citeshttps://doi.org/10.1016/j.ejmech.2007.09.005openalex-snapshot
Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation
inferred← citeshttps://doi.org/10.1016/j.ejps.2020.105258openalex-snapshot
Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens
inferred← citeshttps://doi.org/10.1016/j.ejps.2020.105387openalex-snapshot
Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics
inferred← citeshttps://doi.org/10.1016/j.exppara.2023.108497openalex-snapshot
Immunogenic multi-epitope-based vaccine development to combat cyclosporiasis of immunocompromised patients applying computational biology method
inferred← citeshttps://doi.org/10.1016/j.fsi.2022.08.002openalex-snapshot
In silico prediction of B and T cell epitopes of infectious salmon anemia virus proteins and molecular modeling of T cell epitopes to salmon major histocompatibility complex (MHC) class I
inferred← citeshttps://doi.org/10.1016/j.gene.2016.01.024openalex-snapshot
Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1016/j.gene.2024.149132openalex-snapshot
Synergistic toxicity of compound heterozygous mutations in the COL4A3 gene causes end-stage renal disease in A large family of Alport syndrome
inferred← citeshttps://doi.org/10.1016/j.heliyon.2025.e42014openalex-snapshot
Computational design, expression, and characterization of a Plasmodium falciparum multi-epitope, multi-stage vaccine candidate (PfCTMAG)
inferred← citeshttps://doi.org/10.1016/j.ica.2013.04.023openalex-snapshot
Binding of aquo-ethylenediaminetetraacetatoruthenium(III) to apo-transferrin. Fluorescence, antiproliferative and in silico studies
inferred← citeshttps://doi.org/10.1016/j.ica.2015.04.036openalex-snapshot
Interaction of rhenium(I) complex carrying long alkyl chain with Calf Thymus DNA: Cytotoxic and cell imaging studies
inferred← citeshttps://doi.org/10.1016/j.ica.2018.12.009openalex-snapshot
Synthesis, structural investigations and pharmacological properties of a new zinc complex with a N4-donor Schiff base incorporating 2-pyridyl ring
inferred← citeshttps://doi.org/10.1016/j.ica.2020.119450openalex-snapshot
Bis- and mixed-ligand copper(II) complexes of nalidixic acid the antibacterial drug: Mode of nalidixate coordination determines DNA binding and cleavage and cytotoxicity
inferred← citeshttps://doi.org/10.1016/j.idairyj.2014.03.013openalex-snapshot
Investigations towards understanding the thermal denaturation of lactoperoxidase
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2017.08.047openalex-snapshot
Structural basis for Cullins and RING component inhibition: Targeting E3 ubiquitin pathway conductors for cancer therapeutics
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.147688openalex-snapshot
A retrospective computational validation of a clinically evaluated recombinant envelope protein tetravalent dengue vaccine
inferred← citeshttps://doi.org/10.1016/j.imu.2023.101276openalex-snapshot
Design of a novel multi-epitopes based vaccine against brucellosis
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107575openalex-snapshot
Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress
inferred← citeshttps://doi.org/10.1016/j.jbiotec.2023.12.010openalex-snapshot
In silico designing and characterization of outer membrane protein K (OmpK) from Vibrio anguillarum and its expression in Nicotiana tabacum for the development of a plant-based vaccine against fish vibriosis
inferred← citeshttps://doi.org/10.1016/j.jceh.2017.12.010openalex-snapshot
Structural and Epitope Analysis (T- and B-Cell Epitopes) of Hepatitis C Virus (HCV) Glycoproteins: An in silico Approach
inferred← citeshttps://doi.org/10.1016/j.jcis.2020.03.034openalex-snapshot
Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site
inferred← citeshttps://doi.org/10.1016/j.jfoodeng.2017.04.033openalex-snapshot
A bottom-up approach for encapsulation of sour cherries anthocyanins by using β-lactoglobulin as matrices
inferred← citeshttps://doi.org/10.1016/j.jfoodeng.2017.10.019openalex-snapshot
Investigations on binding mechanism of bioactives from elderberry ( Sambucus nigra L.) by whey proteins for efficient microencapsulation
inferred← citeshttps://doi.org/10.1016/j.jinorgbio.2022.112088openalex-snapshot
In vitro anti-Leishmania activity of new isomeric cobalt(II)complexes and in silico insights: Mitochondria impairment and apoptosis-like cell death of the parasite
inferred← citeshttps://doi.org/10.1016/j.jlumin.2018.07.017openalex-snapshot
Binding mechanisms between lycopene extracted from tomato peels and bovine β-lactoglobulin
inferred← citeshttps://doi.org/10.1016/j.jlumin.2018.08.078openalex-snapshot
Synthesis, photophysics and the binding studies of rhenium(I) diimine surfactant complexes with serum albumins: A spectroscopic and docking study approach
inferred← citeshttps://doi.org/10.1016/j.jmb.2011.11.006openalex-snapshot
Cholesterol Promotes the Interaction of Alzheimer β-Amyloid Monomer with Lipid Bilayer
inferred← citeshttps://doi.org/10.1016/j.jmb.2015.07.016openalex-snapshot
Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
inferred← citeshttps://doi.org/10.1016/j.jmb.2026.169997openalex-snapshot
An Interaction Domain Drives Heme Exchange in the C. albicans CFEM Hemophores Cascade
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.03.008openalex-snapshot
Insight into structural and biochemical determinants of substrate specificity of PFI1625c: Correlation analysis of protein-peptide molecular models
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.004openalex-snapshot
Characterization of ICAM-1 biophore to design cytoadherence blocking peptides
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.04.001openalex-snapshot
Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein–protein docking results
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.04.024openalex-snapshot
Targeted inhibition of Klotho binding to fibroblast growth factor 23 prevents hypophosphetemia
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