| Year |
Citation |
Score |
| 2024 |
Basciu A, Athar M, Kurt H, Neville C, Malloci G, Muredda FC, Bosin A, Ruggerone P, Bonvin AMJJ, Vargiu AV. Predicting binding events in very flexible, allosteric, multi-domain proteins. Biorxiv : the Preprint Server For Biology. PMID 38895346 DOI: 10.1101/2024.06.02.597018 |
0.516 |
|
| 2024 |
Elia Venanzi NA, Basciu A, Vargiu AV, Kiparissides A, Dalby PA, Dikicioglu D. Machine Learning Integrating Protein Structure, Sequence, and Dynamics to Predict the Enzyme Activity of Bovine Enterokinase Variants. Journal of Chemical Information and Modeling. 64: 2681-2694. PMID 38386417 DOI: 10.1021/acs.jcim.3c00999 |
0.387 |
|
| 2023 |
Gervasoni S, Mehla J, Bergen CR, Leus IV, Margiotta E, Malloci G, Bosin A, Vargiu AV, Lomovskaya O, Rybenkov VV, Ruggerone P, Zgurskaya HI. Molecular determinants of avoidance and inhibition of MexB efflux pump. Mbio. e0140323. PMID 37493633 DOI: 10.1128/mbio.01403-23 |
0.325 |
|
| 2022 |
Gervasoni S, Malloci G, Bosin A, Vargiu AV, Zgurskaya HI, Ruggerone P. Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of . Physical Chemistry Chemical Physics : Pccp. PMID 35766032 DOI: 10.1039/d2cp00951j |
0.331 |
|
| 2021 |
Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Computational and Structural Biotechnology Journal. 20: 252-260. PMID 35024097 DOI: 10.1016/j.csbj.2021.11.042 |
0.348 |
|
| 2021 |
Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Computational and Structural Biotechnology Journal. 20: 252-260. PMID 35024097 DOI: 10.1016/j.csbj.2021.11.042 |
0.348 |
|
| 2021 |
Jandova Z, Vargiu AV, Bonvin AMJJ. Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue. Journal of Chemical Theory and Computation. PMID 34342983 DOI: 10.1021/acs.jctc.1c00336 |
0.508 |
|
| 2021 |
Basciu A, Vargiu AV, Malloci G, Ruggerone P, Bonvin AM. In Silico Generation of Holo-Like Conformations of Very Flexible Allosteric Proteins Bearing Multiple Binding Sites Biophysical Journal. 120: 115a-116a. DOI: 10.1016/J.BPJ.2020.11.916 |
0.407 |
|
| 2020 |
Basciu A, Malloci G, Koukos P, Pietrucci F, Bonvin AM, Vargiu AV. EDES: A Protocol to Generate Holo-Like and Druggable Protein Conformations Starting from the APO Structure Biophysical Journal. 118: 44a. DOI: 10.1016/j.bpj.2019.11.420 |
0.579 |
|
| 2019 |
Basciu A, Koukos PI, Malloci G, Bonvin AMJJ, Vargiu AV. Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31720895 DOI: 10.1007/s10822-019-00244-6 |
0.537 |
|
| 2019 |
Basciu A, Malloci G, Pietrucci F, Bonvin AMJJ, Vargiu AV. Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. Journal of Chemical Information and Modeling. PMID 30883122 DOI: 10.1021/acs.jcim.8b00730 |
0.554 |
|
| 2017 |
Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P. Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters. Scientific Reports. 7: 8075. PMID 28808284 DOI: 10.1038/s41598-017-08747-8 |
0.324 |
|
| 2017 |
Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P. Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters. Scientific Reports. 7: 8075. PMID 28808284 DOI: 10.1038/s41598-017-08747-8 |
0.324 |
|
| 2015 |
Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U. Computational study of correlated domain motions in the AcrB efflux transporter. Biomed Research International. 2015: 487298. PMID 25685792 DOI: 10.1155/2015/487298 |
0.32 |
|
| 2012 |
Vargiu AV, Nikaido H. Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 109: 20637-20642. PMID 23175790 DOI: 10.1016/J.Bpj.2012.11.1598 |
0.356 |
|
| 2011 |
Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P. Molecular motions in drug design: the coming age of the metadynamics method. Journal of Computer-Aided Molecular Design. 25: 395-402. PMID 21327922 DOI: 10.1007/S10822-011-9415-3 |
0.359 |
|
| 2011 |
Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P. Molecular motions in drug design: the coming age of the metadynamics method. Journal of Computer-Aided Molecular Design. 25: 395-402. PMID 21327922 DOI: 10.1007/S10822-011-9415-3 |
0.359 |
|
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