EDP Sciences logo
Subscriber Authentication Point
Rechercher
Menu

Articles citing this article

The Citing articles tool gives a list of articles citing the current article.
The citing articles come from EDP Sciences database, as well as other publishers participating in CrossRef Cited-by Linking Program. You can set up your personal account to receive an email alert each time this article is cited by a new article (see the menu on the right-hand side of the abstract page).

Cited article:

Solvent accessible surface area normalized protein–water hydrogen bonds define protein folded state stability and amyloid formation

Prasun Pal, Rahul Debnath, Biman Jana and Sandipan Chakraborty
Physical Chemistry Chemical Physics 28 (6) 4321 (2026)
https://doi.org/10.1039/D5CP04425A

Solvation enhances folding cooperativity and the topology dependence of folding rates in a lattice protein model

Nhung T. T. Nguyen, Pham Nam Phong, Duy Manh Le, Minh-Tien Tran and Trinh Xuan Hoang
The Journal of Chemical Physics 162 (14) (2025)
https://doi.org/10.1063/5.0257315

G-quadruplexes catalyze protein folding by reshaping the energetic landscape

Zijue Huang, Kingshuk Ghosh, Frederick Stull and Scott Horowitz
Proceedings of the National Academy of Sciences 122 (6) (2025)
https://doi.org/10.1073/pnas.2414045122

Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

Naoto Hori and D Thirumalai
Nucleic Acids Research 51 (19) 10737 (2023)
https://doi.org/10.1093/nar/gkad755

Synergetic Effects of Alanine and Glycine in Blob-Based Methods for Predicting Protein Folding Times

Remi Casier and Jean Duhamel
The Journal of Physical Chemistry B 127 (6) 1325 (2023)
https://doi.org/10.1021/acs.jpcb.2c08155

Appraisal of blob-Based Approaches in the Prediction of Protein Folding Times

Remi Casier and Jean Duhamel
The Journal of Physical Chemistry B 127 (41) 8852 (2023)
https://doi.org/10.1021/acs.jpcb.3c04958

Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity

Delaney M. Anderson, Lakshmi P. Jayanthi, Shachi Gosavi and Elizabeth M. Meiering
Frontiers in Molecular Biosciences 10 (2023)
https://doi.org/10.3389/fmolb.2023.1021733

Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo

Yonghyun Song, D. Thirumalai and Changbong Hyeon
Proceedings of the National Academy of Sciences 119 (49) (2022)
https://doi.org/10.1073/pnas.2209422119

Protein folding problem: enigma, paradox, solution

Alexei V. Finkelstein, Natalya S. Bogatyreva, Dmitry N. Ivankov and Sergiy O. Garbuzynskiy
Biophysical Reviews 14 (6) 1255 (2022)
https://doi.org/10.1007/s12551-022-01000-1

Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein

Zhenxing Liu and D. Thirumalai
The Journal of Physical Chemistry B 126 (50) 10684 (2022)
https://doi.org/10.1021/acs.jpcb.2c07093

Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins

Prasun Pal, Sandipan Chakraborty and Biman Jana
The Journal of Physical Chemistry B 126 (51) 10822 (2022)
https://doi.org/10.1021/acs.jpcb.2c05367

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain

Khatuna Kachlishvili, Anatolii Korneev, Luka Maisuradze, Jiaojiao Liu, Harold A. Scheraga, Alexander Molochkov, Patrick Senet, Antti J. Niemi and Gia G. Maisuradze
The Journal of Physical Chemistry B 124 (19) 3855 (2020)
https://doi.org/10.1021/acs.jpcb.0c00628

Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones

D. Thirumalai, George H. Lorimer and Changbong Hyeon
Protein Science 29 (2) 360 (2020)
https://doi.org/10.1002/pro.3795

Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps

Amir Bitran, William M. Jacobs, Xiadi Zhai and Eugene Shakhnovich
Proceedings of the National Academy of Sciences 117 (3) 1485 (2020)
https://doi.org/10.1073/pnas.1913207117

Solution of Levinthal’s Paradox and a Physical Theory of Protein Folding Times

Dmitry N. Ivankov and Alexei V. Finkelstein
Biomolecules 10 (2) 250 (2020)
https://doi.org/10.3390/biom10020250

Dramatic Shape Changes Occur as Cytochrome c Folds

Serdal Kirmizialtin, Felicia Pitici, Alfredo E. Cardenas, Ron Elber and D. Thirumalai
The Journal of Physical Chemistry B 124 (38) 8240 (2020)
https://doi.org/10.1021/acs.jpcb.0c05802

Measuring the average shape of transition paths during the folding of a single biological molecule

Noel Q. Hoffer, Krishna Neupane, Andrew G. T. Pyo and Michael T. Woodside
Proceedings of the National Academy of Sciences 116 (17) 8125 (2019)
https://doi.org/10.1073/pnas.1816602116

Trends in Biomathematics: Modeling, Optimization and Computational Problems

Alexei V. Finkelstein, Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, et al.
Trends in Biomathematics: Modeling, Optimization and Computational Problems 391 (2018)
https://doi.org/10.1007/978-3-319-91092-5_27

Mechanobiology: protein refolding under force

Armando del Río Hernández, Ionel Popa and Ronen Berkovich
Emerging Topics in Life Sciences 2 (5) 687 (2018)
https://doi.org/10.1042/ETLS20180044

A topological order parameter for describing folding free energy landscapes of proteins

Pham Dang Lan, Maksim Kouza, Andrzej Kloczkowski and Mai Suan Li
The Journal of Chemical Physics 149 (17) (2018)
https://doi.org/10.1063/1.5050483

Transition-path properties for folding reactions in the limit of small barriers

Andrew G. T. Pyo, Noel Q. Hoffer, Krishna Neupane and Michael T. Woodside
The Journal of Chemical Physics 149 (11) (2018)
https://doi.org/10.1063/1.5046692

Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover

Naoto Hori, Natalia A. Denesyuk and D. Thirumalai
The Journal of Physical Chemistry B 122 (49) 11279 (2018)
https://doi.org/10.1021/acs.jpcb.8b07129

Dynamics of Disordered Proteins under Confinement: Memory Effects and Internal Friction

Atanu Das and Dmitrii E. Makarov
The Journal of Physical Chemistry B 122 (39) 9049 (2018)
https://doi.org/10.1021/acs.jpcb.8b06112

Folding PDZ2 Domain Using the Molecular Transfer Model

Zhenxing Liu, Govardhan Reddy and D. Thirumalai
The Journal of Physical Chemistry B 120 (33) 8090 (2016)
https://doi.org/10.1021/acs.jpcb.6b00327

Role of Proteome Physical Chemistry in Cell Behavior

Kingshuk Ghosh, Adam M. R. de Graff, Lucas Sawle and Ken A. Dill
The Journal of Physical Chemistry B 120 (36) 9549 (2016)
https://doi.org/10.1021/acs.jpcb.6b04886

Designed protein reveals structural determinants of extreme kinetic stability

Aron Broom, S. Martha Ma, Ke Xia, Hitesh Rafalia, Kyle Trainor, Wilfredo Colón, Shachi Gosavi and Elizabeth M. Meiering
Proceedings of the National Academy of Sciences 112 (47) 14605 (2015)
https://doi.org/10.1073/pnas.1510748112

Colloquium: Random first order transition theory concepts in biology and physics

T. R. Kirkpatrick and D. Thirumalai
Reviews of Modern Physics 87 (1) 183 (2015)
https://doi.org/10.1103/RevModPhys.87.183

Prediction of the optimal set of contacts to fold the smallest knotted protein

P Dabrowski-Tumanski, A I Jarmolinska and J I Sulkowska
Journal of Physics: Condensed Matter 27 (35) 354109 (2015)
https://doi.org/10.1088/0953-8984/27/35/354109

Dissecting Ubiquitin Folding Using the Self-Organized Polymer Model

Govardhan Reddy and D. Thirumalai
The Journal of Physical Chemistry B 119 (34) 11358 (2015)
https://doi.org/10.1021/acs.jpcb.5b03471

Reduction of the Search Space for the Folding of Proteins at the Level of Formation and Assembly of Secondary Structures: A New View on the Solution of Levinthal′s Paradox

Alexei V. Finkelstein and Sergiy O. Garbuzynskiy
ChemPhysChem 16 (16) 3375 (2015)
https://doi.org/10.1002/cphc.201500700

Time to Overcome the High, Long and Bumpy Free-Energy Barrier in a Multi-Stage Process: The Generalized Steady-State Approach

Alexei V. Finkelstein
The Journal of Physical Chemistry B 141205141218004 (2014)
https://doi.org/10.1021/jp5109703

Capturing protein folding-relevant topology via absolute contact order variants

Amy S. Wagaman and Sheila S. Jaswal
Journal of Theoretical and Computational Chemistry 13 (01) 1450005 (2014)
https://doi.org/10.1142/S0219633614500059

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

Rui Zhou, Gia G. Maisuradze, David Suñol, Toni Todorovski, Maria J. Macias, Yi Xiao, Harold A. Scheraga, Cezary Czaplewski and Adam Liwo
Proceedings of the National Academy of Sciences 111 (51) 18243 (2014)
https://doi.org/10.1073/pnas.1420914111

Estimating the Time of Crossing a High, Long and Arbitrary Bumpy Free Energy Barrier

A.V. Finkelstein and А.В. Финкельштейн
Математическая биология и биоинформатика 9 (2) 518 (2014)
https://doi.org/10.17537/2014.9.518

Golden triangle for folding rates of globular proteins

Sergiy O. Garbuzynskiy, Dmitry N. Ivankov, Natalya S. Bogatyreva and Alexei V. Finkelstein
Proceedings of the National Academy of Sciences 110 (1) 147 (2013)
https://doi.org/10.1073/pnas.1210180110

Protein folding: from theory to practice

D Thirumalai, Zhenxing Liu, Edward P O’Brien and Govardhan Reddy
Current Opinion in Structural Biology 23 (1) 22 (2013)
https://doi.org/10.1016/j.sbi.2012.11.010

Coarse‐grained models of protein folding as detailed tools to connect with experiments

Athi N. Naganathan
WIREs Computational Molecular Science 3 (5) 504 (2013)
https://doi.org/10.1002/wcms.1133

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome

Prajwal Ciryam, Richard I. Morimoto, Michele Vendruscolo, Christopher M. Dobson and Edward P. O’Brien
Proceedings of the National Academy of Sciences 110 (2) (2013)
https://doi.org/10.1073/pnas.1213624110

Unfolded protein ensembles, folding trajectories, and refolding rate prediction

A. Das, B. K. Sin, A. R. Mohazab and S. S. Plotkin
The Journal of Chemical Physics 139 (12) (2013)
https://doi.org/10.1063/1.4817215

Why and how does native topology dictate the folding speed of a protein?

Mark Rustad and Kingshuk Ghosh
The Journal of Chemical Physics 137 (20) (2012)
https://doi.org/10.1063/1.4767567

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

Jin Wang, Ronaldo J. Oliveira, Xiakun Chu, Paul C. Whitford, Jorge Chahine, Wei Han, Erkang Wang, José N. Onuchic and Vitor B.P. Leite
Proceedings of the National Academy of Sciences 109 (39) 15763 (2012)
https://doi.org/10.1073/pnas.1212842109

A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology

Thomas J. Lane and Vijay S. Pande
The Journal of Physical Chemistry B 116 (23) 6764 (2012)
https://doi.org/10.1021/jp212332c

Theory of the Molecular Transfer Model for Proteins with Applications to the Folding of the src-SH3 Domain

Zhenxing Liu, Govardhan Reddy and D. Thirumalai
The Journal of Physical Chemistry B 116 (23) 6707 (2012)
https://doi.org/10.1021/jp211941b

Nucleation‐based prediction of the protein folding rate and its correlation with the folding nucleus size

Oxana V. Galzitskaya and Anna V. Glyakina
Proteins: Structure, Function, and Bioinformatics 80 (12) 2711 (2012)
https://doi.org/10.1002/prot.24156

Direct observation of kinetic traps associated with structural transformations leading to multiple pathways of S-layer assembly

Seong-Ho Shin, Sungwook Chung, Babak Sanii, Luis R. Comolli, Carolyn R. Bertozzi and James J. De Yoreo
Proceedings of the National Academy of Sciences 109 (32) 12968 (2012)
https://doi.org/10.1073/pnas.1201504109

Physical limits of cells and proteomes

Ken A. Dill, Kingshuk Ghosh and Jeremy D. Schmit
Proceedings of the National Academy of Sciences 108 (44) 17876 (2011)
https://doi.org/10.1073/pnas.1114477108

Are Peptides Good Two-State Folders?

Alexander M. Berezhkovskii, Florentina Tofoleanu and Nicolae-Viorel Buchete
Journal of Chemical Theory and Computation 7 (8) 2370 (2011)
https://doi.org/10.1021/ct200281d

Bacterial proteins fold faster than eukaryotic proteins with simple folding kinetics

O. V. Galzitskaya, N. S. Bogatyreva and A. V. Glyakina
Biochemistry (Moscow) 76 (2) 225 (2011)
https://doi.org/10.1134/S000629791102009X

Integrated prediction of protein folding and unfolding rates from only size and structural class

David De Sancho and Victor Muñoz
Physical Chemistry Chemical Physics 13 (38) 17030 (2011)
https://doi.org/10.1039/c1cp20402e

Predicting Protein Folding Rate From Amino Acid Sequence

Jian-Xiu GUO, Ni-Ni RAO, Guang-Xiong LIU, Jie LI and Yun-He WANG
PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 37 (12) 1331 (2011)
https://doi.org/10.3724/SP.J.1206.2010.00380

Predicting protein folding rates using the concept of Chou's pseudo amino acid composition

Jianxiu Guo, Nini Rao, Guangxiong Liu, Yong Yang and Gang Wang
Journal of Computational Chemistry 32 (8) 1612 (2011)
https://doi.org/10.1002/jcc.21740

Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins

Zhenxing Liu, Govardhan Reddy, Edward P. O’Brien and D. Thirumalai
Proceedings of the National Academy of Sciences 108 (19) 7787 (2011)
https://doi.org/10.1073/pnas.1019500108

Collapse Dynamics of Single Proteins Extended by Force

Ronen Berkovich, Sergi Garcia-Manyes, Michael Urbakh, Joseph Klafter and Julio M. Fernandez
Biophysical Journal 98 (11) 2692 (2010)
https://doi.org/10.1016/j.bpj.2010.02.053

Evidence for Initial Non-specific Polypeptide Chain Collapse During the Refolding of the SH3 Domain of PI3 Kinase

Amrita Dasgupta and Jayant B. Udgaonkar
Journal of Molecular Biology 403 (3) 430 (2010)
https://doi.org/10.1016/j.jmb.2010.08.046

Navigating the Downhill Protein Folding Regime via Structural Homologues

Athi N. Naganathan, Peng Li, Raúl Perez-Jimenez, Jose M. Sanchez-Ruiz and Victor Muñoz
Journal of the American Chemical Society 132 (32) 11183 (2010)
https://doi.org/10.1021/ja103612q

How the diffusivity profile reduces the arbitrariness of protein folding free energies

M. Hinczewski, Y. von Hansen, J. Dzubiella and R. R. Netz
The Journal of Chemical Physics 132 (24) (2010)
https://doi.org/10.1063/1.3442716

Is protein folding rate dependent on number of folding stages? Modeling of protein folding with ferredoxin-like fold

O. V. Galzitskaya
Biochemistry (Moscow) 75 (6) 717 (2010)
https://doi.org/10.1134/S0006297910060064

Coupling between Properties of the Protein Shape and the Rate of Protein Folding

Dmitry N. Ivankov, Natalya S. Bogatyreva, Michail Yu Lobanov, Oxana V. Galzitskaya and Michael Levitt
PLoS ONE 4 (8) e6476 (2009)
https://doi.org/10.1371/journal.pone.0006476

Refolding dynamics of stretched biopolymers upon force quench

Changbong Hyeon, Greg Morrison, David L. Pincus and D. Thirumalai
Proceedings of the National Academy of Sciences 106 (48) 20288 (2009)
https://doi.org/10.1073/pnas.0905764106

Direct observation of an ensemble of stable collapsed states in the mechanical folding of ubiquitin

Sergi Garcia-Manyes, Lorna Dougan, Carmen L. Badilla, Jasna Brujić and Julio M. Fernández
Proceedings of the National Academy of Sciences 106 (26) 10534 (2009)
https://doi.org/10.1073/pnas.0901213106

An experimental survey of the transition between two-state and downhill protein folding scenarios

Feng Liu, Deguo Du, Amelia A. Fuller, Jennifer E. Davoren, Peter Wipf, Jeffery W. Kelly and Martin Gruebele
Proceedings of the National Academy of Sciences 105 (7) 2369 (2008)
https://doi.org/10.1073/pnas.0711908105

Brownian dynamics simulation of polymer collapse in a poor solvent: influence of implicit hydrodynamic interactions

Tri Thanh Pham, Mohit Bajaj and J. Ravi Prakash
Soft Matter 4 (6) 1196 (2008)
https://doi.org/10.1039/b717350d

Сonnection of Shape of Globular Proteins with their Folding and Unfolding Rates

N.S. Bogatyreva and Н.С. Богатырева
Математическая биология и биоинформатика 3 (2) 69 (2008)
https://doi.org/10.17537/2008.3.69

Exploiting the downhill folding regime via experiment

Victor Muñoz, Mourad Sadqi, Athi N. Naganathan and David de Sancho
HFSP Journal 2 (6) 342 (2008)
https://doi.org/10.2976/1.2988030

Probing the mechanisms of fibril formation using lattice models

Mai Suan Li, D. K. Klimov, J. E. Straub and D. Thirumalai
The Journal of Chemical Physics 129 (17) (2008)
https://doi.org/10.1063/1.2989981

Folding of tandem‐linked domains

E. Prabhu Raman, Valeri Barsegov and Dmitri K. Klimov
Proteins: Structure, Function, and Bioinformatics 67 (4) 795 (2007)
https://doi.org/10.1002/prot.21339

Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy

Kirstin A. Walther, Frauke Gräter, Lorna Dougan, Carmen L. Badilla, Bruce J. Berne and Julio M. Fernandez
Proceedings of the National Academy of Sciences 104 (19) 7916 (2007)
https://doi.org/10.1073/pnas.0702179104

Ultrafast dynamics of protein collapse from single-molecule photon statistics

Daniel Nettels, Irina V. Gopich, Armin Hoffmann and Benjamin Schuler
Proceedings of the National Academy of Sciences 104 (8) 2655 (2007)
https://doi.org/10.1073/pnas.0611093104

Force-Clamp Spectroscopy of Single-Protein Monomers Reveals the Individual Unfolding and Folding Pathways of I27 and Ubiquitin

Sergi Garcia-Manyes, Jasna Brujić, Carmen L. Badilla and Julio M. Fernández
Biophysical Journal 93 (7) 2436 (2007)
https://doi.org/10.1529/biophysj.107.104422

Mechanical control of the directional stepping dynamics of the kinesin motor

Changbong Hyeon and José N. Onuchic
Proceedings of the National Academy of Sciences 104 (44) 17382 (2007)
https://doi.org/10.1073/pnas.0708828104

Contour Length and Refolding Rate of a Small Protein Controlled by Engineered Disulfide Bonds

Sri Rama Koti Ainavarapu, Jasna Brujić, Hector H. Huang, et al.
Biophysical Journal 92 (1) 225 (2007)
https://doi.org/10.1529/biophysj.106.091561

Entropy capacity determines protein folding

Oxana V. Galzitskaya and Sergiy O. Garbuzynskiy
Proteins: Structure, Function, and Bioinformatics 63 (1) 144 (2006)
https://doi.org/10.1002/prot.20851

Optimal ratio between the average conformational entropy and the average energy of interaction between residues for fast protein folding

O. V. Galzitskaya and S. A. Garbuzinskii
Biophysics 51 (4) 554 (2006)
https://doi.org/10.1134/S0006350906040075

Reversible Thermal Denaturation of a 60-kDa Genetically Engineered β-Sheet Polypeptide

Igor K. Lednev, Vladimir V. Ermolenkov, Seiichiro Higashiya, Ludmila A. Popova, Natalya I. Topilina and John T. Welch
Biophysical Journal 91 (10) 3805 (2006)
https://doi.org/10.1529/biophysj.106.082792