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■ Abbreviation / Long Form : MM-PBSA / molecular mechanics Poisson-Boltzmann surface area

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Total Number of Papers: 281
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Abbreviation:   MM-PBSA  (>> Co-occurring Abbreviation)
Long Form:   molecular mechanics Poisson-Boltzmann surface area
 Abbreviation Variation
 Long Form Variation
 Pair(Abbreviation/Long Form) Variation
No. Year Title Co-occurring Abbreviation
2022 GPR109A, HA, PAs
2022 MD
2022 Alpha-mangostin as an inhibitor of GSK3β in triple-negative breast cancer. TNBC
2022 An insight from computational approach to explore novel, high-affinity phosphodiesterase 10A inhibitors for neurological disorders. MD, PDE10A, PKA
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
2022 Computational discovery of small drug-like compounds as potential inhibitors of PD-1/PD-L1 interactions. MD, PD-1, PD-L1
2022 Computational Investigation of Structural Basis for Enhanced Binding of Isoflavone Analogues with Mitochondrial Aldehyde Dehydrogenase. HB, MD
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
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