Pablo Chacón - Related publications

Affiliations: 
Institute of Physical Chemistry Rocasolano (CSIC) 
NOTE: We are testing a new system for identifying relevant work based on semantic analysis that identifies similarities between recently published papers and the current author's publications. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches.
50 most relevant papers in past 60 days:
Year Citation  Score
2021 Zweckstetter M. NMR hawk-eyed view of AlphaFold2 structures. Protein Science : a Publication of the Protein Society. PMID 34469019 DOI: 10.1002/pro.4175   
2021 Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XIV. Proteins. PMID 34533838 DOI: 10.1002/prot.26237   
2021 Seong K, Krasileva K. Computational structural genomics unravels common folds and novel families in the secretome of fungal phytopathogen . Molecular Plant-Microbe Interactions : Mpmi. PMID 34415195 DOI: 10.1094/MPMI-03-21-0071-R   
2021 Egbert M, Ghani U, Ashizawa R, Kotelnikov S, Nguyen T, Desta I, Hashemi N, Padhorny D, Kozakov D, Vajda S. Assessing the binding properties of CASP14 targets and models. Proteins. PMID 34368994 DOI: 10.1002/prot.26209   
2021 Sun Z, Zheng S, Zhao H, Niu Z, Lu Y, Pan Y, Yang Y. To improve the predictions of binding residues with DNA, RNA, carbohydrate, and peptide via multi-task deep neural networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34637380 DOI: 10.1109/TCBB.2021.3118916   
2021 Tanramluk D*, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure. PMID 34614393 DOI: 10.1016/j.str.2021.09.004   
2021 Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. Journal of the American Chemical Society. PMID 34637297 DOI: 10.1021/jacs.1c06837   
2021 Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Frontiers in Molecular Biosciences. 8: 716973. PMID 34497831 DOI: 10.3389/fmolb.2021.716973   
2021 Miao Z, Wang Q, Xiao X, Kamal GM, Song L, Zhang X, Li C, Zhou X, Jiang B, Liu M. CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts. Journal of Biomolecular Nmr. PMID 34510297 DOI: 10.1007/s10858-021-00383-9   
2021 Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J. Modeling SARS-CoV2 proteins in the CASP-commons experiment. Proteins. PMID 34462960 DOI: 10.1002/prot.26231   
2021 Škrbić T, Hoang TX, Giacometti A, Maritan A, Banavar JR. Spontaneous dimensional reduction and ground state degeneracy in a simple chain model. Physical Review. E. 104: L012101. PMID 34412247 DOI: 10.1103/PhysRevE.104.L012101   
2021 Hassan M, Coutsias EA. Kinematic Reconstruction of Cyclic Peptides and Protein Backbones from Partial Data. Journal of Chemical Information and Modeling. PMID 34570494 DOI: 10.1021/acs.jcim.1c00453   
2021 Nakamura T, Yokaichiya T, Fedorov DG. Quantum-Mechanical Structure Optimization of Protein Crystals and Analysis of Interactions in Periodic Systems. The Journal of Physical Chemistry Letters. 8757-8762. PMID 34478310 DOI: 10.1021/acs.jpclett.1c02510   
2021 Cao Y, Das P, Chenthamarakshan V, Chen PY, Melnyk I, Shen Y. Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design. Proceedings of Machine Learning Research. 139: 1261-1271. PMID 34423306   
2021 Pearce NM, Gros P. A method for intuitively extracting macromolecular dynamics from structural disorder. Nature Communications. 12: 5493. PMID 34535675 DOI: 10.1038/s41467-021-25814-x   
2021 Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Frontiers in Molecular Biosciences. 8: 707661. PMID 34532343 DOI: 10.3389/fmolb.2021.707661   
2021 Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. Journal of Biomolecular Structure & Dynamics. 1-15. PMID 34499020 DOI: 10.1080/07391102.2021.1975568   
2021 Michael E, Simonson T. How much can physics do for protein design? Current Opinion in Structural Biology. 72: 46-54. PMID 34461593 DOI: 10.1016/j.sbi.2021.07.011   
2021 Malliavin TE. Tandem domain structure determination based on a systematic enumeration of conformations. Scientific Reports. 11: 16925. PMID 34413388 DOI: 10.1038/s41598-021-96370-z   
2021 T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. The Journal of Physical Chemistry. B. PMID 34423989 DOI: 10.1021/acs.jpcb.1c01227   
2021 Ye L, Wu P, Peng Z, Gao J, Liu J, Yang J. Improved estimation of model quality using predicted inter-residue distance. Bioinformatics (Oxford, England). PMID 34473228 DOI: 10.1093/bioinformatics/btab632   
2021 Zhu Y, Ye F, Zhou Z, Liu W, Liang Z, Hu G. Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions. Molecules (Basel, Switzerland). 26. PMID 34500587 DOI: 10.3390/molecules26175153   
2021 Wiggers F, Wohl S, Dubovetskyi A, Rosenblum G, Zheng W, Hofmann H. Diffusion of a disordered protein on its folded ligand. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34504002 DOI: 10.1073/pnas.2106690118   
2021 Feng N, Feng H, Wang S, Punekar AS, Ladenstein R, Wang DC, Zhang Q, Ding J, Liu W. Structures of heat shock factor trimers bound to DNA. Iscience. 24: 102951. PMID 34458700 DOI: 10.1016/j.isci.2021.102951   
2021 Skolnick J, Gao M, Zhou H, Singh S. AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. Journal of Chemical Information and Modeling. PMID 34586808 DOI: 10.1021/acs.jcim.1c01114   
2021 Peterson TA, Piper RC. Deconvolution of Multiple Rab Binding Domains Using the Batch Yeast 2-Hybrid Method DEEPN. Methods in Molecular Biology (Clifton, N.J.). 2293: 117-141. PMID 34453714 DOI: 10.1007/978-1-0716-1346-7_9   
2021 Voith von Voithenberg L, Barth A, Trauschke V, Demarco B, Tyagi S, Koehler C, Lemke EA, Lamb DC. Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34389669 DOI: 10.1073/pnas.2025578118   
2021 Yang Z, Chakraborty M, White AD. Predicting chemical shifts with graph neural networks. Chemical Science. 12: 10802-10809. PMID 34476061 DOI: 10.1039/d1sc01895g   
2021 Li Q, Kang C. Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines. 9. PMID 34440248 DOI: 10.3390/biomedicines9081044   
2021 Pinkston J, Jo J, Olsen KJ, Comer D, Glaittli CA, Loria JP, Johnson SJ, Hengge AC. Significant Loop Motions in the SsoPTP Protein Tyrosine Phosphatase Allow for Dual General Acid Functionality. Biochemistry. PMID 34496202 DOI: 10.1021/acs.biochem.1c00365   
2021 Liu W, Li C, Shan J, Wang Y, Chen G. Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration. Royal Society Open Science. 8: 210160. PMID 34457335 DOI: 10.1098/rsos.210160   
2021 Taujale R, Zhou Z, Yeung W, Moremen KW, Li S, Kannan N. Mapping the glycosyltransferase fold landscape using interpretable deep learning. Nature Communications. 12: 5656. PMID 34580305 DOI: 10.1038/s41467-021-25975-9   
2021 Gervasoni S, Spencer J, Hinchliffe P, Pedretti A, Vairoletti F, Mahler G, Mulholland AJ. A multiscale approach to predict the binding mode of metallo beta-lactamase inhibitors. Proteins. PMID 34455628 DOI: 10.1002/prot.26227   
2021 Wang Q, Wang L, Zhang Y, Zhang X, Zhang L, Shang W, Bai F. Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications. Journal of Medicinal Chemistry. PMID 34415156 DOI: 10.1021/acs.jmedchem.1c00320   
2021 Parkman JA, Barksdale CA, Michaelis DJ. CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations. Journal of Computational Chemistry. PMID 34411332 DOI: 10.1002/jcc.26729   
2021 Koukos PI, Réau M, Bonvin AMJJ. Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of Chemical Information and Modeling. PMID 34436890 DOI: 10.1021/acs.jcim.1c00796   
2021 Bandera AM, Bartho J, Lammens K, Drexler DJ, Kleinschwärzer J, Hopfner KP, Witte G. BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture. Nucleic Acids Research. PMID 34432045 DOI: 10.1093/nar/gkab736   
2021 Ashraf S, Ranaghan KE, Woods CJ, Mulholland AJ, Ul-Haq Z. Exploration of the structural requirements of Aurora Kinase B inhibitors by a combined QSAR, modelling and molecular simulation approach. Scientific Reports. 11: 18707. PMID 34548506 DOI: 10.1038/s41598-021-97368-3   
2021 Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallographica. Section D, Structural Biology. 77: 1168-1182. PMID 34473087 DOI: 10.1107/S2059798321008196   
2021 Bustamante A, Rivera R, Floor M, Babul J, Baez M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophysical Journal. PMID 34555362 DOI: 10.1016/j.bpj.2021.09.026   
2021 Murata H, Imakawa H, Koga N, Chikenji G. The register shift rules for βαβ-motifs for de novo protein design. Plos One. 16: e0256895. PMID 34460870 DOI: 10.1371/journal.pone.0256895   
2021 Liu W, Chen J, Jin L, Liu ZY, Lu M, Jiang G, Yang Q, Quan C, Nam KH, Xu Y. Functional and structural analysis of catabolite control protein C that responds to citrate. Scientific Reports. 11: 20285. PMID 34645869 DOI: 10.1038/s41598-021-99552-x   
2021 Asthana P, Singh D, Pedersen JS, Hynönen MJ, Sulu R, Murthy AV, Laitaoja M, Jänis J, Riley LW, Venkatesan R. Structural insights into the substrate-binding proteins Mce1A and Mce4A from . Iucrj. 8: 757-774. PMID 34584737 DOI: 10.1107/S2052252521006199   
2021 Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34475217 DOI: 10.1073/pnas.2106195118   
2021 Lv TM, Chen DL, Liang JJ, Bai M, Lin B, Huang XX, Ma GX, Song SJ. Structural Revisions of Two Highly Aromatic Naphthoquinone-Derived Dimers Based on NMR Analysis, Computer-Assisted Structure Elucidation Methods, and Computations. Organic Letters. PMID 34436914 DOI: 10.1021/acs.orglett.1c02626   
2021 Fowler NJ, Sljoka A, Williamson MP. The accuracy of NMR protein structures in the Protein Data Bank. Structure (London, England : 1993). PMID 34331857 DOI: 10.1016/j.str.2021.07.001   
2021 Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers. e23471. PMID 34498740 DOI: 10.1002/bip.23471   
2021 Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. International Journal of Molecular Sciences. 22. PMID 33498210 DOI: 10.3390/ijms22030997   
2021 Toyama Y, Harkness RW, Kay LE. Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34446566 DOI: 10.1073/pnas.2111257118   
2021 Dunce JM, Salmon LJ, Davies OR. Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12. Nature Structural & Molecular Biology. 28: 681-693. PMID 34373646 DOI: 10.1038/s41594-021-00636-z