Journal Club archive¶
Every paper presented at the BIOKT journal club, newest first. Presenters are identified by initials.
Transcribed from the group website in October 2026; citations are as entered there, with errors corrected against Crossref.
2026¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2026-10-13 | DDS | Scalable Constant pH Molecular Dynamics in GROMACS. N. Aho, P. Buslaev, A. Jansen, P. Bauer, G. Groenhof & B. Hess. J. Chem. Theory Comput. 18, 10, 6148–6160 (2022). | 10.1021/acs.jctc.2c00516 |
| 2026-10-06 | LA | Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, XH···π, and M+···π contacts. A. Campo-Cacharrón, E. M. Cabaleiro-Lago, J. A. Carrazana-García & J. Rodríguez-Otero. J. Comput. Chem. 35, 17, 1290–1301 (2014). | 10.1002/jcc.23623 |
| 2026-09-29 | JCJ | The role of distant mutations and allosteric regulation on LovD active site dynamics. G. Jiménez-Osés, S. Osuna, X. Gao, M. R. Sawaya, L. Gilson, S. J. Collier, G. W. Huisman, T. O. Yeates, Y. Tang & K. N. Houk. Nat. Chem. Biol. 10, 431–436 (2014). | 10.1038/nchembio.1503 |
| 2026-09-22 | SS | DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles. G. Tesei, J. M. Martins, M. B. A. Kunze, Y. Wang, R. Crehuet & K. Lindorff-Larsen. PLoS Comput. Biol. 17, 1, e1008551 (2021). | 10.1371/journal.pcbi.1008551 |
| 2026-09-15 | DR | pH-Dependent Protonation of the Phl p 6 Pollen Allergen Studied by NMR and cpH-aMD. F. Hofer, V. Dietrich, A. S. Kamenik, M. Tollinger & K. R. Liedl. J. Chem. Theory Comput. 15, 10, 5716–5726 (2019). | 10.1021/acs.jctc.9b00540 |
| 2026-06-16 | SS | Water-directed pinning is key to tau prion formation, M.P. Vigers,S. Lobo,S. Najafi,A. Dubose,K. Tsay,P. Ganguly,A.P. Longhini,Y. Jin,S.K. Buratto,K.S. Kosik,M.S. Shell,J. Shea, & S. Han. Proc. Natl. Acad. Sci. U.S.A. 122 (18) e2421391122, (2025). | 10.1073/pnas.2421391122 |
| 2026-05-05 | S | Biomolecular Condensates Dictate the Folding Landscape of Proteins. N. Hess & J. A. Joseph. BioRxiv. (2026). | 10.64898/2026.01.12.699095 |
| 2026-03-17 | JU | Biomolecular Condensates Act as Distinct Solvation Environments that Reshape Amino Acid pKa Values. S. Rekhi, & J. Mittal. BioRxiv (2026). | 10.64898/2026.01.11.698869 |
| 2026-02-17 | JCJ | Binding Entropy Can Be Predicted by Crystallographic Ensembles. C. A. Miller, & S. A. Wankowicz. BioRxiv (2026). | 10.64898/2026.01.19.699807 |
| 2026-01-26 | S | How the Extent of Protein Folding and Oligomerization Modulate Condensate Formation and Properties I. Edelstein & Y. Levy. J. Phys. Chem. Lett. 16 11248–11258 (2025). | 10.1021/acs.jpclett.5c02083 |
2025¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2025-11-25 | AU | Site-saturation mutagenesis of 500 human protein domains. Beltran, A., Jiang, X., Shen, Y. et al. Nature 637, 885–894 (2025). | 10.1038/s41586-024-08370-4 |
| 2025-11-04 | JCJ | Improving conformational ensembles of folded proteins in GoMartini. Kalutskii et al, BioRxiv (2025). | 10.1101/2025.10.24.684331 |
| 2025-10-14 | JA | The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables Rizzi et al. J. Phys. Chem. Lett. (2025) 16, 37, 9636–9645. | 10.1021/acs.jpclett.5c02079 |
| 2025-09-23 | DDS | Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Joseph et al. Nat Comput Sci. (2021) 1 (11): 732–743. | 10.1038/s43588-021-00155-3 |
| 2025-09-12 | DGO | Improving pKa Predictions with Reparameterized Force Fields and Free Energy Calculations. C. J. Wilson, V. Gapsys, B. L. de Groot. J. Chem. Theory Comput. (2025), 21, 8, 4095–4106. | 10.1021/acs.jctc.5c00031 |
| 2025-03-28 | DSB | A coarse-grained model for simulations of phosphorylated disordered proteins. A. S. Rauh, G. Stausbøll Hedemark, G. Tesei & K. Lindorff-Larsen. bioRxiv (2025). | 10.1101/2025.03.19.644261 |
| 2025-02-14 | AU | The mechanism of amyloid fibril growth from Φ-value analysis. Larsen, J.A., Barclay, A., Vettore, N. et al. Nat. Chem. (2025). | 10.1038/s41557-024-01712-9 |
| 2025-02-07 | DDS | Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. Wei, MT., Elbaum-Garfinkle, S., Holehouse, A. et al. Nature Chem. 9, 1118–1125 (2017). | 10.1038/nchem.2803 |
| 2025-01-09 | JA | Stereochemistry in the disorder–order continuum of protein interactions. E. A. Newcombe, A. D. Due, Sottini, A. et al.. Nature 636, 762–768 (2024). | 10.1038/s41586-024-08271-6 |
2024¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2024-11-29 | JA | Accurate de novo design of high-affinity protein binding macrocycles using deep learning. S. A. Rettie, D. Juergens, V. Adebomi et al. bioRxiv 2024.11.18.622547. | 10.1101/2024.11.18.622547 |
| 2024-11-22 | JCJ | OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field. K. B. Pedersen, L. Borges-Araújo, A. D. Stange, P. C. T. Souza, S. J. Marrink & B. Schiøtt. J. Chem. Theory Comput. 2024, 20, 18, 8049–8070. | 10.1021/acs.jctc.4c00553 |
| 2024-11-08 | DDS | Machine-guided path sampling to discover mechanisms of molecular self-organization. H. Jung, R. Covino, A. Arjun, C. Leitold, C. Dellago, P. G. Bolhuis & G. Hummer. Nat. Comput. Sci. 3, 334–345 (2023). | 10.1038/s43588-023-00428-z |
| 2024-10-18 | DGO | Desensitization dynamics of the AMPA receptor. J. Aittoniemi, M. Ø. Jensen, A. C. Pan & D. E. Shaw. Structure 31, 724-734 (2023). | 10.1016/j.str.2023.03.013 |
| 2024-09-27 | DSB | Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions. R. S. Paton & J. M. Goodman. J. Chem. Inf. Model., 49, 4, 944–955 (2009). | 10.1021/ci900009f |
| 2024-08-01 | AU | On the role of native contact cooperativity in protein folding. D. Wang, L. B. Frechette & R. B. Best. Proc. Natl. Acad. Sci. USA, 121, e2319249121 (2024). | 10.1073/pnas.2319249121 |
| 2024-07-24 | JA | Assessing the Performance of Peptide Force Fields for Modeling the Solution Structural Ensembles of Cyclic Peptides. J. Miao, A. P. Ghosh, M. Ngoc Ho, C. Li, X. Huang, B. L. Pentelute, J. D. Baleja, and Y. S. Lin. J. Phys. Chem. B. 128, 22, 5281–5292 (2024). | 10.1021/acs.jpcb.4c00157 |
| 2024-06-27 | DDS | Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins. S. Das, YH. Lin, R. M. Vernon, J. D. Forman-Kay & H. Sun Chan. Proc. Natl. Acad. Sci. USA. 117 (46) 28795-28805 (2020). | 10.1073/pnas.2008122117 |
| 2024-06-20 | AU | NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions. R. A. Boto, F. Peccati, R. Laplaza, C. Quan, A. Carbone, JP. Piquemal, Y. Maday & J. Contreras-Garcı́a. J. Chem. Theory Comput., 16, 7, 4150–4158 (2020). | 10.1021/acs.jctc.0c00063 |
| 2024-04-29 | JCJ | Modulating the Coupling Efficiency of P450 BM3 by Controlling Water Diffusion through Access Tunnel Engineering. Shuaiqi Meng, Yu Ji, Luo Liu, Mehdi D. Davari, Ulrich Schwaneberg. ChemSusChem. 15, 9, e202102434 (2022). | 10.1002/cssc.202102434 |
| 2024-02-16 | DSB | The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. W. G. Noid; Jhih-Wei Chu; G. S. Ayton; V. Krishna; S. Izvekov; G. A. Voth; Avisek Das; Hans C. Andersen. J. Chem. Phys. 128, 244114, (2008). | 10.1063/1.2938860 |
| 2024-02-02 | JU | H Atom Positions and Nuclear Magnetic Resonance Chemical Shifts of Short H Bonds in Photoactive Yellow Protein. K. Saito & H. Ishikita. Biochemistry , 51, 1171–1177, (2012). | 10.1021/bi201877e |
2023¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2023-12-12 | DSB | TorchMD: A Deep Learning Framework for Molecular Simulations. Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, and Gianni De Fabritiis*. J. Chem. Theory Comput. , 17, 4, 2355–2363 (2021). | 10.1021/acs.jctc.0c01343 |
| 2023-11-17 | DDS | Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2. Alderson et al. Proc. Natl. Acad. Sci. USA (2023) 120 (44) e2304302120. | 10.1073/pnas.2304302120 |
| 2023-11-03 | AFC | Enhanced statistical sampling reveals microscopic complexity in the talin mechanosensor folding energy landscape. Rafael Tapia-Rojo et al. Nat. Phys. 19, 52-60 (2023). | 10.1038/s41567-022-01808-4 |
| 2023-09-29 | JA | Predicting and interpreting large-scale mutagenesis data using analyses of protein stability and conservation. M. Haraldson Høie, M. Cagiada et al. Cell Reports 38, 110207 (2022). | 10.1016/j.celrep.2021.110207 |
| 2023-09-22 | DSB | Machine learning coarse-grained potentials of protein thermodynamics. Majewski, M., Pérez, A., Thölke, P. et al. Nat. Commun. 14, 5739 (2023). | 10.1038/s41467-023-41343-1 |
| 2023-09-15 | DDS | Extreme dynamics in a biomolecular condensate. Galvanetto et al. Nature 619, 876–883 (2023). | 10.1038/s41586-023-06329-5 |
| 2023-06-23 | DDS | Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations. Y. Zhang, X.Liu, & J. Chen. J. Chem. Theory Comput. 19, 5 (2023). | 10.1021/acs.jctc.2c01139 |
| 2023-05-26 | MFP | Resource-efficient quantum algorithm for protein folding. A. Robert, P. Kl. Barkoutsos, S. Woerner & I. Tavernelli npj Quantum Information 7, 38 (2021). | 10.1038/s41534-021-00368-4 |
| 2023-04-28 | JA | A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. M. Bazayeva, A. Giachetti,M. Pagliai A. Rosato. Int. J. Mol. Sci., 24, 5440 (2023). | 10.3390/ijms24065440 |
| 2023-03-31 | AFC | Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. M. C. R. Melo, D. E. B. Gomes & R. C. Bernardi. J. Am. Chem. Soc., 145, 1, 70–77 (2023). | 10.1021/jacs.2c07674 |
| 2023-03-17 | DSB | Rapid prediction and analysis of protein intrinsic disorder. G. W. Dayhoff II, V. N. Uversky, Protein Sci., 31, 12 (2022). | 10.1002/pro.4496 |
| 2023-02-17 | DDS | Metainference: A Bayesian inference method for heterogeneous systems. M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo. Science Advances, 2, 1 (2016). | 10.1126/sciadv.1501177 |
| 2023-02-03 | MFP | Aging can transform single-component protein condensates into multiphase architectures. A. Garaizar, J. R. Espinosa, J. A. Joseph, G. Krainer, Y. Shen, T. P.J. Knowles, and R. Collepardo-Guevara. Proc. Natl. Acad. Sci. U.S.A. 119, e2119800119 (2022). | 10.1073/pnas.2119800119 |
2022¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2022-12-02 | DSB | Statistical proofs of the interdependence between nearest neighbor effects on polypeptide backbone conformations. J. González-Delgado, P. Bernadó, P. Neuvial & J. Cortés. J. Struct. Biol. 214, 107907 (2022). | 10.1016/j.jsb.2022.107907 |
| 2022-11-11 | JA | Small molecules targeting the disordered transactivation domain of the androgen receptor induce the formation of collapsed helical states. Zhu, Salvatella & Robustelli. Nat. Commun. 13, 6390 (2022). | 10.1038/s41467-022-34077-z |
| 2022-11-04 | AFC | Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. S. M. Sedlak et al. Nano Letters. 19, 3415-3421 (2019). | 10.1021/acs.nanolett.8b04045 |
| 2022-10-07 | DDS | Self-Effected Allosteric Coupling and Cooperativity in Hypoxic Response Regulation with Disordered Proteins. B. Wen et al. J. Phys. Chem. Lett. 13, 9201-9209 (2022). | 10.1021/acs.jpclett.2c02065 |
| 2022-09-16 | DSB | Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions. Y. Zhang, X. Liu & J. Chen. J. Chem. Inf. Model. (2022). | 10.1021/acs.jcim.2c00974 |
| 2022-06-17 | JA | Assessment of models for calculating the hydrodynamic radius of intrinsically disordered proteins. F. Pesce, E. A. Newcombe, P. Seiffert, E. E. Tranchant, J. G. Olsen, B. B. Kragelund, K. Lindorff-Larsen. BioRxiv. (2022). | 10.1101/2022.06.11.495732 |
| 2022-06-10 | DDS | Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan. V. Gapsys, S. Michielssens, D. Seeliger & B. L. de Groot. Angew. Chem. Int. Ed. 2016. | 10.1002/anie.201510054 |
| 2022-06-03 | AFC | Optimal Sacrificial Domains in Mechanical Polyproteins: S. epidermidis Adhesins Are Tuned for Work Dissipation. H. Liu, Z. Liu, B. Yang, J. Lopez Morales & M. A. Nash. JACS Au. 2022. | 10.1021/jacsau.2c00121 |
| 2022-05-27 | DSB | Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon. A. A. Rosenberg, A. Marx & A. M. Bronstein. Nat. Commun. 13, 2815 (2022). | 10.1038/s41467-022-30390-9 |
| 2022-05-13 | IR | Understanding p300-transcription factor interactions using sequence variation and hybridization. F. Hóbor, Z. Hegedüs, A. Avila Ibarra, V. L. Petrovicz, G. J. Bartlett, R. B. Sessions, A. J. Wilson & T. A. Edwards. RSC Chem. Biol., 2022, 3, 592-603. | 10.1039/D2CB00026A |
| 2022-04-29 | JA | Integrating Molecular Simulation and Experimental Data: A Bayesian/Maximum Entropy Reweighting Approach. Bottaro S., Bengtsen T., Lindorff-Larsen K. (2020) In: Gáspári Z. (eds) Structural Bioinformatics. Methods in Molecular Biology, vol 2112. | 10.1007/978-1-0716-0270-6_15 |
| 2022-04-01 | DDS | Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Tesei et al, Proc. Natl. Acad. Sci. USA, 118, e2111696118 (2021). | 10.1073/pnas.2111696118 |
| 2022-03-04 | IM | SpookyNet: Learning force fields with electronic degrees of freedom and nonlocal effects. Unke et al. Nat. Commun. 2021, 12, 7273. | 10.1038/s41467-021-27504-0 |
| 2022-02-18 | AFC | Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. Bernardi et al. J. Am. Chem. Soc. 2019, 141, 14752-14763. | 10.1021/jacs.9b06776 |
| 2022-02-04 | IR | Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2. X. Qin, H. Chen, L. Tu, Y. Ma, N. Liu, H. Zhang, D. Li, B. Riedl, D. Bierer, F. Yin & Z. Li. J. Med. Chem. 2021, 64, 13693–13703. | 10.1021/acs.jmedchem.1c01043 |
| 2022-01-21 | DSB | How multisite phosphorylation impacts the conformations of intrinsically disordered proteins. F. Jin & F. Gräter. PLoS Comput. Biol. 2021, 17, e1008939. | 10.1371/journal.pcbi.1008939 |
| 2022-01-14 | JA | Diffusion of a disordered protein on its folded ligand. F. Wiggers, S. Wohl, A. Dubovetskyi, G. Rosenblum, W. Zheng & H. Hofmann. PNAS, 2021, 118, e2106690118. | 10.1073/pnas.2106690118 |
2021¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2021-11-26 | IM | Deep learning the slow modes for rare events sampling. Bonati, Piccini & Parrinello. PNAS, 2021, 118, e2113533118. | 10.1073/pnas.2113533118 |
| 2021-11-12 | DDS | A short peptide synthon for liquid–liquid phase separation. Abbas, M., Lipiński, W.P., Nakashima, K.K. et al. Nat. Chem. 2021, 13, 1046–1054. | 10.1038/s41557-021-00788-x |
| 2021-10-15 | DSB | Highly accurate protein structure prediction with AlphaFold. J. Jumper et al. Nature 2021, 596, 583–589. | 10.1038/s41586-021-03819-2 |
| 2021-10-08 | AFC | Streptavidin/biotin: Tethering geometry defines unbinding mechanics. S. M. Sedlak, L. C. Schendel, H. E. Gaub & R. C. Bernardi. Science Adv. 2020, 6. | 10.1126/sciadv.aay5999 |
| 2021-10-01 | IM | What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. E. Suárez, R. P. Wiewiora, C. Wehmeyer, F. Noé, J. D. Chodera and D. M. Zuckerman. J. Chem. Theory Comput. 2021, 17, 3119–3133. | 10.1021/acs.jctc.0c01154 |
| 2021-09-23 | DDS | Quantification of Conformational Entropy Unravels Effect of Disordered Flanking Region in Coupled Folding and Binding. F. F. Theisen, L. Staby, F. G. Tidemand, C. O’Shea, A. Prestel, M. Willemoës, B. B. Kragelund & K. Skriver. J. Am. Chem. Soc. 2021, 143, 14540–14550. | 10.1021/jacs.1c04214 |
| 2021-07-16 | MFP | Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints. T. J. Giese & D. M. York. J. Chem. Theory Comput. 2021, 17, 1326–1336. | 10.1021/acs.jctc.0c01219 |
| 2021-07-09 | JA | Zinc Coordination Spheres in Protein Structures. M. Laitaoja, J. Valjakka & J.Jänis. Inorg. Chem. 2013, 52, 10983–10991. | 10.1021/ic401072d |
| 2021-07-02 | AFC | Calcium stabilizes the strongest protein fold. L. F. Milles, E. M. Unterauer, T. Nicolaus & H. E. Gaub. Nat. Commun. 2018, 9, 4764. | 10.1038/s41467-018-07145-6 |
| 2021-06-25 | IR | Intrinsic disorder is essential for Cas9 inhibition of anti-CRISPR AcrIIA5. SY An, D Ka, I Kim, EH Kim, NK Kim, E Bae, JY Suh. Nucleic Acids Res. 2020, 48, 7584–7594. | 10.1093/nar/gkaa512 |
| 2021-06-18 | DSB | Cyclic peptides: backbone rigidification and capability of mimicking motifs at protein–protein interfaces. H. Huang, J. Damjanovic, J. Miao & YS Lin. Phys. Chem. Chem. Phys. 2021, 23, 607-616. | 10.1039/D0CP04633G |
| 2021-06-11 | IM | Conformational Entropy as Collective Variable for Proteins. F. Palazzesi, O. Valsson & M. Parrinello. J. Phys. Chem. Lett. 2017, 8, 4752–4756. | 10.1021/acs.jpclett.7b01770 |
| 2021-06-04 | DDS | High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme. R. Appadurai, J. Nagesh & A. Srivastava. Nat. Commun. 2021, 12, 958. | 10.1038/s41467-021-21105-7 |
| 2021-05-28 | DSB | Configurational entropy of native proteins. M. Karplus, T. Ichiye & B. M. Pettitt. Biophys J. 1987, 52 (1083-5). | 10.1016/S0006-3495(87)83303-9 |
| 2021-05-21 | MFP | On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. M. Pechlaner, C. Oostenbrink, W. F. van Gunsteren. J. Comput. Chem. 2021. | 10.1002/jcc.26541 |
| 2021-05-07 | IR | Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning. B Narayan, N-V. Buchete & R. Elber. J. Phys. Chem. B. 2021. | 10.1021/acs.jpcb.1c00264 |
| 2021-04-30 | IM | Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. M. I. Zimmerman, J. R. Porter, X. Sun, R. R. Silva, and G. R. Bowman. J. Chem. Theory Comput. 2018, 14, 11, (5459–5475). | 10.1021/acs.jctc.8b00500 |
| 2021-04-16 | AFC | Molecular mechanism of extreme mechanostability in a pathogen adhesin. L. F. Milles, K. Schulten, H. E. Gaub, R. C. Bernardi. Science, 2018, 359, (1527-1533). | 10.1126/science.aar2094 |
| 2021-04-09 | JA | Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. S. Bottaro, G. Bussi, S. D. Kennedy & D.H. Turner, Sci. Adv., 2018, 4. | 10.1126/sciadv.aar8521 |
| 2021-03-26 | DSB | Understanding Conformational Entropy in Small Molecules. L. Chan, G. M. Morris & G. R. Hutchison. JCTC, 2021. | 10.1021/acs.jctc.0c01213 |
| 2021-03-12 | DDS | Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. E. W. Martin, A. S. Holehouse, I. Peran, M. Farag, J. Incicco, A. Bremer, C. R. Grace, A. Soranno, R. V. Pappu & T. Mittag. Science. 2020, 367, 694-699. | 10.1126/science.aaw8653 |
| 2021-02-26 | MFP | Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation. S. Ekesan & D. M. York. J. Phys. Chem. B 2019, 123, 22, 4611–4624. | 10.1021/acs.jpcb.8b11923 |
| 2021-02-19 | IR | Unraveling the Molecular Mechanism of Prion H2 C-Terminus Misfolding by Metadynamics Simulations. Z. Xu, H. Liu, S. Wang, Q. Zhang, X. Yao, S. Zhou & H. Liu. ACS Chem. Neurosci. 2020, 11, 5, 772–782. | 10.1021/acschemneuro.9b00679 |
| 2021-02-05 | IM | Canonical sampling through velocity rescaling. G. Bussi, D. Donadio and M. Parrinello J. Chem. Phys. 126, 014101 (2007). | 10.1063/1.2408420 |
| 2021-01-29 | DSB | Effects of Ions and Small Compounds on the Structure of Aβ42 Monomers. F. Mahmoudinobar, B. L. Nilsson and C. L. Dias. J. Phys. Chem. B. 2021. | 10.1021/acs.jpcb.0c09617 |
| 2021-01-22 | DDS | Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations, W. Zheng, G. L. Dignon, N. Jovic, X. Xu, R. M. Regy, N. L. Fawzi, Y. C. Kim, R. B. Best, and J. Mittal. J. Phys. Chem. B 2020, 124, 51, 11671–11679. | 10.1021/acs.jpcb.0c10489 |
| 2021-01-15 | MFP | Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods T. J. Giese and D. M. York*. JCTC 2019, 15, 10, 5543–5562. | 10.1021/acs.jctc.9b00401 |
2020¶
| Date | Presenter | Paper | DOI |
|---|---|---|---|
| 2020-12-11 | DSB | Calculation of Configurational Entropy Differences from Conformational Ensembles Using Gaussian Mixture, G. Gyimesi, P. Závodszky & A. Szilágy, JCTC 13, 29-41 (2017). | 10.1021/acs.jctc.6b00837 |
| 2020-12-04 | IR | Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes. J. R. Abella, D. Antunes, K. Jackson, G. Lizee, C. Clementi & L. E. Kavraki. PNAS 117, 30610–30618 (2020). | 10.1073/pnas.2007246117 |
| 2020-11-27 | IM | Adaptive Markov state model estimation using short reseeding trajectories. H. Wan and V. A. Voelz. J. Chem. Phys. 152, 024103 (2020). | 10.1063/1.5142457 |
| 2020-11-20 | MFP | Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease. G. T. Heller, F. A. Aprile, T. C. T. Michaels, R. Limbocker, M. Perni, F. S. Ruggeri, B. Mannini, T. Löhr, M. Bonomi, C. Camilloni, A. De Simone, I. C. Felli, R. Pierattelli, T. P. J. Knowles, C. M. Dobson and M. Vendruscolo. Sci. Advances (2020). | 10.1126/sciadv.abb5924 |
| 2020-11-06 | DSB | In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides. D. Li and R. Brüschweiler. Phys. Rev. Lett. (2009). | 10.1103/PhysRevLett.102.118108 |
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