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[Related PubMed/MEDLINE]
Total Number of Papers: 281
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| Abbreviation |
: MM-PBSA |
| Long Form |
: molecular mechanics Poisson-Boltzmann surface area |
|
| No. |
Year |
Title |
Co-occurring Abbreviation |
| 1 |
2022 |
|
GPR109A, HA, PAs |
| 2 |
2022 |
|
MD |
| 3 |
2022 |
Alpha-mangostin as an inhibitor of GSK3β in triple-negative breast cancer. |
TNBC |
| 4 |
2022 |
An insight from computational approach to explore novel, high-affinity phosphodiesterase 10A inhibitors for neurological disorders. |
MD, PDE10A, PKA |
| 5 |
2022 |
Calcium Ion Binding to the Mutants of Calmodulin: A Structure-Based Computational Predictive Model of Binding Affinity Using a Charge Scaling Approach in Molecular Dynamics Simulation. |
CaM, CBPs, WT |
| 6 |
2022 |
Computational discovery of small drug-like compounds as potential inhibitors of PD-1/PD-L1 interactions. |
MD, PD-1, PD-L1 |
| 7 |
2022 |
Computational Investigation of Structural Basis for Enhanced Binding of Isoflavone Analogues with Mitochondrial Aldehyde Dehydrogenase. |
HB, MD |
| 8 |
2022 |
Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods. |
ACE-2, atv, COVID-19, MD, prz, RBD, SARS-CoV-2, VOC |
| 9 |
2022 |
Computer-based identification of olive oil components as a potential inhibitor of neirisaral adhesion a regulatory protein. |
DFT, FMOs, MD, NadR |
| 10 |
2022 |
Consensus docking and MM-PBSA computations identify putative furin protease inhibitors for developing potential therapeutics against COVID-19. |
AUC, BEDROC, COVID-19, Pa, ROC, SARS-CoV-2 |
| 11 |
2022 |
Deciphering the binding mechanism of inhibitors of the SARS-CoV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes. |
DCCM, FEL, Mpro, MR-aMD, PCA |
| 12 |
2022 |
Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes. |
--- |
| 13 |
2022 |
Development of antithrombotic peptides based on the molecular interactions between von Willebrand factor and GPIbα. |
MD, vWF |
| 14 |
2022 |
Evaluation of decursin and its isomer decursinol angelate as potential inhibitors of human glutamate dehydrogenase activity through in silico and enzymatic assay screening. |
DA, DN, EGCG, MD |
| 15 |
2022 |
Exploring Structural Mechanism of COVID-19 Treatment with Glutathione as a Potential Peptide Inhibitor to the Main Protease: Molecular Dynamics Simulation and MM/PBSA Free Energy Calculations Study. |
MD, MDS, MEV, Mpro, RR |
| 16 |
2022 |
Exploring the Binding Process of Cognate Ligand to Add Adenine Riboswitch Aptamer by Using Explicit Solvent Molecular Dynamics (MD) Simulation. |
MD |
| 17 |
2022 |
Homology Modeling, de Novo Design of Ligands, and Molecular Docking Identify Potential Inhibitors of Leishmania donovani 24-Sterol Methyltransferase. |
LdSMT, LELP, Pa, Pi |
| 18 |
2022 |
Immunoinformatics Approach to Design Novel Subunit Vaccine against the Epstein-Barr Virus. |
BCL, CTL, DCC, DSSP, EBV, HTL, PCA, Rg, RMSD, RMSF, TLRs |
| 19 |
2022 |
In silico design of novel quinazoline-based compounds as potential Mycobacterium tuberculosis PknB inhibitors through 2D and 3D-QSAR, molecular dynamics simulations combined with pharmacokinetic predictions. |
CoMSIA, HQSAR, M. tuberculosis, MD, MM-GBSA, PknB |
| 20 |
2022 |
In-silico study of the interactions between acylated glucagon like-peptide-1 analogues and the native receptor. |
FA, GLP-1, GLP-1R, MD |
| 21 |
2022 |
Interaction mechanism of novel fluorescent antifolates targeted with folate receptors α and β via molecular docking and molecular dynamic simulations. |
MD |
| 22 |
2022 |
Investigating effect of mutation on structure and function of G6PD enzyme: a comparative molecular dynamics simulation study. |
--- |
| 23 |
2022 |
Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. |
hACE-2, RBD, VoC's |
| 24 |
2022 |
Molecular dynamics simulations, molecular docking, and kinetics study of kaempferol interaction on Jack bean urease: Comparison of extended solvation model. |
ITC, JBU, KPF, MD |
| 25 |
2022 |
Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies. |
ADMET, DOC, Mpro, PDT, PLpro, SARS-CoV-2 |
| 26 |
2022 |
Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket. |
--- |
| 27 |
2022 |
Repurposing of Doxycycline to Hinder the Viral Replication of SARS-CoV-2: From in silico to in vitro Validation. |
FDA, IHUMI, NTP, RdRp |
| 28 |
2022 |
Some Flavolignans as Potent Sars-Cov-2 Inhibitors via Molecular Docking, Molecular Dynamic Simulations and ADME Analysis. |
MD, RMSD, RMSF, SARS-CoV-2 Mpro |
| 29 |
2022 |
Structural and vibrational investigations and molecular docking studies of a vinca alkoloid, vinorelbine. |
d,p, MEP, MMGBSA, PED |
| 30 |
2022 |
Structural insights into conformational stability and binding of thiazolo-[2,3-b] quinazolinone derivatives with EGFR-TKD and in-vitro study. |
ADMET, EGFR-TKD |
| 31 |
2022 |
Synthesis and Chemopreventive Potential of 5-FU/Genistein Hybrids on Colorectal Cancer Cells. |
MD |
| 32 |
2022 |
Targeting COVID-19 pandemic: in silico evaluation of 2-hydroxy-1, 2-diphenylethanone N(4)-methyl-N(4)-phenylthiosemicarbazone as a potential inhibitor of SARS-CoV-2. |
MD, SARS-CoV-2 |
| 33 |
2022 |
Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1. |
JAK, PTKs, RA, TYK2 |
| 34 |
2021 |
9-Arylimino noscapinoids as potent tubulin binding anticancer agent: chemical synthesis and cellular evaluation against breast tumour cells. |
FEB |
| 35 |
2021 |
Adsorption study of lac dyes with chitosan coated on silk fibroin using molecular dynamics simulations. |
MD |
| 36 |
2021 |
Alemtuzumab scFv fragments and CD52 interaction study through molecular dynamics simulation and binding free energy. |
scFv |
| 37 |
2021 |
An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: molecular dynamics simulation, principal component analysis and binding free energy calculation study. |
PCA |
| 38 |
2021 |
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro. |
AD4, FEP, FPL, LIE, Mpro |
| 39 |
2021 |
Biomimetic design of inhibitors of immune checkpoint LILRB4. |
AML, LILRB4, MD |
| 40 |
2021 |
Computational drug repurposing study elucidating simultaneous inhibition of entry and replication of novel corona virus by Grazoprevir. |
ACE-2, COVID-19, HCV, MD, RdRp, TMPRSS2 |
| 41 |
2021 |
Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. |
AUC, COVID-19, MAPK, Pa, Pi, ROC |
| 42 |
2021 |
Computational Study on Potential Novel Anti-Ebola Virus Protein VP35 Natural Compounds. |
AUC, EBOV, EBOV VP35, MD, Pa, Pi, ROC |
| 43 |
2021 |
Computational-aided design: minimal peptide sequence to block dengue virus transmission into cells. |
DV |
| 44 |
2021 |
Could Peganum harmala be effective in the treatment of COVID-19? |
GC-MS, RdRp |
| 45 |
2021 |
Destabilization of Abeta fibrils by omega-3 polyunsaturated fatty acids: a molecular dynamics study. |
AD, EPA, LNL, PUFAs, RMSD, SASA |
| 46 |
2021 |
DFT, molecular docking and molecular dynamics simulation studies on some newly introduced natural products for their potential use against SARS-CoV-2. |
ADME, DFT, MD |
| 47 |
2021 |
Drug-Drug Interaction Between Oxycodone and Diazepam by a Combined in Silico Pharmacokinetic and Pharmacodynamic Modeling Approach. |
DDIs, DZP, KOR, MD, MOR, OXY, PBPK, PD, PK |
| 48 |
2021 |
Exploring the toxic effects and mechanism of methoxylated polybrominated diphenyl ethers (MeO-PBDEs) on thyroxine-binding globulin (TBG): Synergy between spectroscopic and computations. |
CD, MeO-PBDEs, TBG, UV-visible |
| 49 |
2021 |
Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRalpha. an In Silico Insight. |
FA, FRalpha, MD, MTX, PTX, RMSD, RMSF |
| 50 |
2021 |
Identification of potential SARS-CoV-2 entry inhibitors by targeting the interface region between the spike RBD and human ACE2. |
ACE2, COVID-19, MD, MM-GBSA, RBD, SARS-CoV-2 |
| 51 |
2021 |
Identification of SARS-CoV-2 inhibitors from extracts of Houttuynia cordata Thunb. |
MM-GBSA, RdRp, SARS, SARS-CoV-2, TCM |
| 52 |
2021 |
In silico analyses of major active constituents of fingerroot (Boesenbergia rotunda) unveils inhibitory activities against SARS-CoV-2 main protease enzyme. |
MM-GBSA, Mpro, SARS-CoV-2 |
| 53 |
2021 |
In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation. |
MD |
| 54 |
2021 |
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. |
hACE2, MD, MM-GBSA, RBD |
| 55 |
2021 |
In silico design of novel FAK inhibitors using integrated molecular docking, 3D-QSAR and molecular dynamics simulation studies. |
CoMFA, CoMSIA, FAK, MD |
| 56 |
2021 |
In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus. |
--- |
| 57 |
2021 |
In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors. |
SARS-CoV-2 Mpro |
| 58 |
2021 |
Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study. |
--- |
| 59 |
2021 |
Key criteria for engineering mycotoxin binding aptamers via computational simulations: Aflatoxin B1 as a case study. |
AFB1, MDS |
| 60 |
2021 |
Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment. |
3CLpro, MM-GBSA, PPs |
| 61 |
2021 |
Molecular docking and dynamics simulation study of bioactive compounds from Ficus carica L. with important anticancer drug targets. |
Bcl-2, CDK2, CDK6, MM-GBSA, topo I, topo II, VEGFR2 |
| 62 |
2021 |
Molecular docking and dynamics studies of cigarette smoke carcinogens interacting with acetylcholinesterase and butyrylcholinesterase enzymes of the central nervous system. |
AChE, BuChE, CNS, CSC, MDS, NNN |
| 63 |
2021 |
Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. |
D. orbita, FDA, hERG, PK, Rg, RMSD, RMSF, SASA, TK |
| 64 |
2021 |
Multi-step molecular docking and dynamics simulation-based screening of large antiviral specific chemical libraries for identification of Nipah virus glycoprotein inhibitors. |
MD, NiV, NiV-G, WHO |
| 65 |
2021 |
Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release. |
FES, HSA, MD, RMSD |
| 66 |
2021 |
Recent Developments in Free Energy Calculations for Drug Discovery. |
LIE, MD |
| 67 |
2021 |
Relaxed complex scheme and molecular dynamics simulation suggests small molecule inhibitor of human TMPRSS2 for combating COVID-19. |
COVID-19, TMPRSS2 |
| 68 |
2021 |
Screening of Azadirachta indica phytoconstituents as GSK-3beta inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study. |
GSK-3, MDS |
| 69 |
2021 |
Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, Mpro and PLpro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. |
Mpro, PLpro |
| 70 |
2021 |
Structure-based design approach of potential BCL-2 inhibitors for cancer chemotherapy. |
ADMET, Bcl-2, MM-GBSA |
| 71 |
2021 |
Synergistic interaction of N-3-Br-benzyl-noscapine and docetaxel abrogates oncogenic potential of breast cancer cells. |
Br-Bn-Nos, DOX, MM-GBSA |
| 72 |
2021 |
The SARS-Cov-2 Proliferation Blocked by a Novel and Potent Main Protease Inhibitor via Computer-aided Drug Design. |
MD |
| 73 |
2021 |
Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents. |
--- |
| 74 |
2021 |
Thermodynamic and structural aspects of molecular recognition in mannose-binding protein complexes: a theoretical study over HRP-ArtinM association. |
gHRP, HRP, MD |
| 75 |
2020 |
Application of MM-PBSA Methods in Virtual Screening. |
VS |
| 76 |
2020 |
Binding Modes and Selectivity of Cannabinoid 1 (CB1) and Cannabinoid 2 (CB2) Receptor Ligands. |
CB, CB1, CB2, ECL, MD, TM |
| 77 |
2020 |
Biomimetic Design of Peptide Neutralizer of Ebola Virus with Molecular Simulation. |
ABM, EBOV, mAb, MD |
| 78 |
2020 |
Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization. |
CBP |
| 79 |
2020 |
De novo design based identification of potential HIV-1 integrase inhibitors: A pharmacoinformatics study. |
MD |
| 80 |
2020 |
Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes. |
--- |
| 81 |
2020 |
Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations. |
AIDS, ATV, DRV, HIV, LPV, TPV |
| 82 |
2020 |
Genetic diversity and in silico evidence of target-site mutation in the EPSPS gene in endowing glyphosate resistance in Eleusine indica (L.) from Malaysia. |
AS-PCR, RIN, SB |
| 83 |
2020 |
How Well Does the Extended Linear Interaction Energy Method Perform in Accurate Binding Free Energy Calculations? |
ELIE, FEP, MD, MM-GBSA, PI, RMSE, TI |
| 84 |
2020 |
Identification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum. |
MD, Pf |
| 85 |
2020 |
In silico characterisation of olive phenolic compounds as potential cyclooxygenase modulators. Part 1. |
1OL, COX, LG2, NSAIDs |
| 86 |
2020 |
Investigation of Binding Affinity between Potential Antiviral Agents and PB2 Protein of Influenza A: Non-equilibrium Molecular Dynamics Simulation Approach. |
SMD |
| 87 |
2020 |
Investigation on the Mechanisms of Synchronous Interaction of K3Cit with Melamine and Uric Acid That Avoids the Formation of Large Clusters. |
MEL, PMFs, UA |
| 88 |
2020 |
Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch. |
AR, MD |
| 89 |
2020 |
Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors. |
CWC |
| 90 |
2020 |
Modeling the Sterol-Binding Domain of Aster-A Provides Insight into Its Multiligand Specificity. |
ER, MB-ASMD, PM |
| 91 |
2020 |
Molecular docking and dynamics simulations studies of OmpATb identifies four potential novel natural product-derived anti-Mycobacterium tuberculosis compounds. |
IFD, OmpATb |
| 92 |
2020 |
Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. |
MD |
| 93 |
2020 |
Molecular docking and molecular dynamics simulations of a mutant Acinetobacter haemolyticus alkaline-stable lipase against tributyrin. |
Asp, Lys, MD, Mut-LipKV1, tributyrin-LipKV1 |
| 94 |
2020 |
Molecular docking and molecular dynamics simulations studies on beta-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation. |
MD, NC, OPL |
| 95 |
2020 |
Multiple Molecular Dynamics Simulations of the Inhibitor GRL-02031 Complex with Wild Type and Mutant HIV-1 Protease Reveal the Binding and Drug-Resistance Mechanism. |
HIV-1, MMD, SIE |
| 96 |
2020 |
Potential of NO donor furoxan as SARS-CoV-2 main protease (Mpro) inhibitors: in silico analysis. |
MD, Mpro, Mpro, NO |
| 97 |
2020 |
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. |
--- |
| 98 |
2020 |
Revealing the Inhibition Mechanism of RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2 by Remdesivir and Nucleotide Analogues: A Molecular Dynamics Simulation Study. |
MD, MESP, RdRp |
| 99 |
2020 |
Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase. |
DYRK1A, PBS |
| 100 |
2020 |
Structure-based identification of natural compound inhibitor against M. tuberculosis thioredoxin reductase: insight from molecular docking and dynamics simulation. |
Mtb, PCA, PCN, TrxR, Trxs |
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