Raul Perez-Jimenez - Related publications

Affiliations: 
2007-2013 Department of Biological Sc Columbia University, New York, NY 
 2013- CIC nanoGUNE 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Campos LA, Sadqi M, Muñoz V. Lessons about Protein Folding and Binding from Archetypal Folds. Accounts of Chemical Research. PMID 32914959 DOI: 10.1021/acs.accounts.0c00322   
2020 Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Scientific Reports. 10: 18211. PMID 33097750 DOI: 10.1038/s41598-020-75239-7   
2020 Tang WS, Fawzi NL, Mittal J. Refining All-Atom Protein Force Fields for Polar-Rich, Prion-like, Low-Complexity Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 33078950 DOI: 10.1021/acs.jpcb.0c07545   
2020 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/acs.jpcb.0c05802   
2020 Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophysical Journal. 119: 978-988. PMID 32758421 DOI: 10.1016/j.bpj.2020.07.015   
2020 Chen X, Rajasekaran N, Liu K, Kaiser CM. Synthesis runs counter to directional folding of a nascent protein domain. Nature Communications. 11: 5096. PMID 33037221 DOI: 10.1038/s41467-020-18921-8   
2020 Kuhar N, Umapathy S. Probing the stepwise unfolding of bovine serum albumin using 2D correlation Raman spectroscopic analysis. Analytical Chemistry. PMID 32865392 DOI: 10.1021/acs.analchem.0c02968   
2020 Bergues-Pupo AE, Lipowsky R, Vila Verde A. Unfolding mechanism and free energy landscape of single, stable, alpha helices at low pull speeds. Soft Matter. PMID 33030193 DOI: 10.1039/d0sm01166e   
2020 Michael E, Polydorides S, Simonson T, Archontis G. Hybrid MC/MD for protein design. The Journal of Chemical Physics. 153: 054113. PMID 32770896 DOI: 10.1063/5.0013320   
2020 Subramanian S, Golla H, Divakar K, Kannan A, De Sancho D, Naganathan AN. Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape? The Journal of Physical Chemistry. B. PMID 32955882 DOI: 10.1021/acs.jpcb.0c05976   
2020 Yu M, Zhao Z, Chen Z, Le S, Yan J. Modulating mechanical stability of heterodimerization between engineered orthogonal helical domains. Nature Communications. 11: 4476. PMID 32900995 DOI: 10.1038/s41467-020-18323-w   
2020 Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Current Opinion in Structural Biology. 64: 145-151. PMID 32795948 DOI: 10.1016/j.sbi.2020.07.003   
2020 Nandi T, Desai A, Ainavarapu SRK. The unfolding transition state of ubiquitin with charged residues has higher energy than that with hydrophobic residues. Physical Chemistry Chemical Physics : Pccp. PMID 33026000 DOI: 10.1039/d0cp03876h   
2020 Gosu V, Shin D, Song KD, Heo J, Oh JD. Molecular modeling and dynamic simulation of chicken Mx protein with the S631N polymorphism. Journal of Biomolecular Structure & Dynamics. 1-10. PMID 32962555 DOI: 10.1080/07391102.2020.1819419   
2020 Hinostroza F, Neely A, Araya-Duran I, Marabolí V, Canan J, Rojas M, Aguayo D, Latorre R, González-Nilo FD, Cárdenas AM. Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures. Scientific Reports. 10: 18151. PMID 33097808 DOI: 10.1038/s41598-020-75216-0   
2020 Di Lena P, Baldi P. Fold recognition by scoring protein maps using the congruence coefficient. Bioinformatics (Oxford, England). PMID 32976564 DOI: 10.1093/bioinformatics/btaa833   
2020 Barozet A, Bianciotto M, Vaisset M, Siméon T, Minoux H, Cortés J. Protein loops with multiple meta-stable conformations: a challenge for sampling and scoring methods. Proteins. PMID 32920900 DOI: 10.1002/prot.26008   
2020 Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry. PMID 32970423 DOI: 10.1021/acs.biochem.0c00533   
2020 Nagpal S, Luong TDN, Sadqi M, Muñoz V. Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers. Acs Synthetic Biology. 9: 2427-2439. PMID 32822536 DOI: 10.1021/acssynbio.0c00190   
2020 Maffucci I, Laage D, Stirnemann G, Sterpone F. Differences in thermal structural changes and melting between mesophilic and thermophilic dihydrofolate reductase enzymes. Physical Chemistry Chemical Physics : Pccp. 22: 18361-18373. PMID 32789320 DOI: 10.1039/d0cp02738c   
2020 Pal S, Banerjee S, Prabhakaran EN. Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth. The Journal of Physical Chemistry. A. PMID 32877193 DOI: 10.1021/acs.jpca.0c05489   
2020 Yan Z, Wang J. Funneled energy landscape unifies principles of protein binding and evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 33067388 DOI: 10.1073/pnas.2013822117   
2020 Mendelman N, Zerbetto M, Buck M, Meirovitch E. Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches. The Journal of Physical Chemistry. B. PMID 32981310 DOI: 10.1021/acs.jpcb.0c05846   
2020 Stojanovski BM, Pelc LA, Zuo X, Di Cera E. Zymogen and activated protein C have similar structural architecture. The Journal of Biological Chemistry. PMID 32855236 DOI: 10.1074/jbc.RA120.014789   
2020 Bozovic O, Zanobini C, Gulzar A, Jankovic B, Buhrke D, Post M, Wolf S, Stock G, Hamm P. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America. PMID 33020277 DOI: 10.1073/pnas.2012999117   
2020 Mohapatra SB, Manoj N. A conserved π-helix plays a key role inthermoadaptation of catalysis in the glycoside hydrolase family 4. Biochimica Et Biophysica Acta. Proteins and Proteomics. 140523. PMID 32853774 DOI: 10.1016/j.bbapap.2020.140523   
2020 Staby L, Kemplen KR, Stein A, Ploug M, Clarke J, Skriver K, Heidarsson PO, Kragelund BB. Disorder in a two-domain neuronal Ca-binding protein regulates domain stability and dynamics using ligand mimicry. Cellular and Molecular Life Sciences : Cmls. PMID 32936312 DOI: 10.1007/s00018-020-03639-z   
2020 Sánchez Rodríguez F, Simpkin AJ, Davies OR, Keegan RM, Rigden DJ. Helical ensembles outperform ideal helices in molecular replacement. Acta Crystallographica. Section D, Structural Biology. 76: 962-970. PMID 33021498 DOI: 10.1107/S205979832001133X   
2020 Vattepu R, Klausmeyer RA, Ayella A, Yadav R, Dille JT, Saiz SV, Beck MR. Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence. Protein Science : a Publication of the Protein Society. PMID 32797644 DOI: 10.1002/pro.3929   
2020 Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. Journal of Medicinal Chemistry. PMID 33017535 DOI: 10.1021/acs.jmedchem.0c01500   
2020 Zhao Y, Zhao Y, Peng B, Zhang L. Dynamic behavior of biomaterials uncovered by cryo-electron microscopy. Combinatorial Chemistry & High Throughput Screening. PMID 33019925 DOI: 10.2174/1386207323666201005100653   
2020 Ramanathan A, Parvatikar A, Chennubhotla SC, Mei Y, Sinha SC. Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain. Biomolecules. 10. PMID 32932757 DOI: 10.3390/biom10091308   
2020 Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science (New York, N.Y.). 369: 1132-1136. PMID 32855341 DOI: 10.1126/science.abc0881   
2020 Ou X, Xue B, Lao Y, Wutthinitikornkit Y, Tian R, Zou A, Yang L, Wang W, Cao Y, Li J. Structure and sequence features of mussel adhesive protein lead to its salt-tolerant adhesion ability. Science Advances. 6. PMID 32978166 DOI: 10.1126/sciadv.abb7620   
2020 Pang Y, Liu B. SelfAT-Fold: protein fold recognition based on residue-based and motif-based self-attention networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 33090951 DOI: 10.1109/TCBB.2020.3031888   
2020 Aoki-Shioi N, Jobichen C, Sivaraman J, Kini RM. Unusual quaternary structure of a homodimeric synergistic-type toxin from mamba snake venom defines its molecular evolution. The Biochemical Journal. PMID 33000863 DOI: 10.1042/BCJ20200529   
2020 Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophysical Journal. PMID 32946768 DOI: 10.1016/j.bpj.2020.08.036   
2020 Singh R, Deshmukh S, Kumar A, Goyal VD, Makde RD. Crystal structure of XCC3289 from Xanthomonas campestris: homology with the N-terminal substrate-binding domain of Lon peptidase. Acta Crystallographica. Section F, Structural Biology Communications. 76: 488-494. PMID 33006577 DOI: 10.1107/S2053230X20011875   
2020 Ryzhov P, Tian Y, Yao Y, Bobkov AA, Im W, Marassi FM. Conformational States of the Cytoprotective Protein Bcl-xL. Biophysical Journal. PMID 32888404 DOI: 10.1016/j.bpj.2020.08.014   
2020 Cheng Y, Zhang Y, Gong Z, Zhang XH, Li Y, Shi X, Pei Y, You H. High Mechanical Stability and Slow Unfolding Rates Are Prevalent in Parallel-Stranded DNA G-Quadruplexes. The Journal of Physical Chemistry Letters. PMID 32885976 DOI: 10.1021/acs.jpclett.0c02229   
2020 Fenner K, Redgate A, Brancaleon L. A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain. Journal of Biomolecular Structure & Dynamics. 1-16. PMID 32909899 DOI: 10.1080/07391102.2020.1817785   
2020 Kamalesh D, Nair A, Sreeshma J, Arundhathi PS, Sudandiradoss C. Statistical and molecular dynamics (MD) simulation approach to investigate the role of intrinsically disordered regions of shikimate dehydrogenase in microorganisms surviving at different temperatures. Extremophiles : Life Under Extreme Conditions. PMID 32975630 DOI: 10.1007/s00792-020-01198-6   
2020 Ozgur B, Sayar M. Representation of the conformational ensemble of peptides in coarse grained simulations. The Journal of Chemical Physics. 153: 054108. PMID 32770883 DOI: 10.1063/5.0012391   
2020 Tsuji T, Yoshinaga S, Takeda M, Sato T, Sonoda A, Ishida N, Yunoki K, Toda E, Terashima Y, Matsushima K, Terasawa H. Rational design of monodispersed mutants of proteins by identifying aggregation contact sites using solubilizing agents. Biochemistry. PMID 32929969 DOI: 10.1021/acs.biochem.0c00414   
2020 Guo Z, Hou J, Cheng J. DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures. Proteins. PMID 32893403 DOI: 10.1002/prot.26007   
2020 Scull NW, Lucius AL. Kinetic Analysis of AAA+ Translocases by Combined Fluorescence and Anisotropy Methods. Biophysical Journal. 119: 1335-1350. PMID 32997959 DOI: 10.1016/j.bpj.2020.08.018   
2020 Chen M, Chen X, Jin S, Lu W, Lin X, Wolynes PG. Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry. B. PMID 32931278 DOI: 10.1021/acs.jpcb.0c06719   
2020 Chen M, Chen X, Jin S, Lu W, Lin X, Wolynes PG. Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry. B. PMID 32931278 DOI: 10.1021/acs.jpcb.0c06719   
2020 Hasan S, Isar M, Naeem A. Macromolecular crowding stabilises native structure of α-chymotrypsinogen-A against hexafluoropropanol-induced aggregates. International Journal of Biological Macromolecules. PMID 32835802 DOI: 10.1016/j.ijbiomac.2020.08.149   
2020 Chakravorty A, Higham J, Henchman RH. Entropy of Proteins Using Multiscale Cell Correlation. Journal of Chemical Information and Modeling. PMID 32955869 DOI: 10.1021/acs.jcim.0c00611