Results 1 to 10 of about 6,813,928 (408)

Protein Photo-folding and Quantum Folding Theory [PDF]

arXiv, 2011
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein photo-folding processes are compared with common protein folding without interaction of photons (nonradiative folding).
Luo, Liaofu
arxiv   +7 more sources

Distance-based Protein Folding Powered by Deep Learning [PDF]

Proceedings of the National Academy of Sciences of the United States of America, 2018
Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed to predict good 3D models from predicted contacts.
Xu, Jinbo
arxiv   +5 more sources

Nucleation phenomena in protein folding: The modulating role of protein sequence [PDF]

J. Physics: Condensed Matter 19 (2007) 285212, 2006
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts ...
Abkevich V I, Abkevich V I, Baldwin R L, Chan H S, Dill K A, Du R, Faisca P F N, Faisca P F N da Gama M M T Ball R C Shakhnovich E I, Fersht A R, Galzitskaya O V, Galzitskaya O V, Go N, Gromiha M M, Gutin A, Gutin A M, Gutin A M, Jackson S E, Karplus M, Kim P S, Klimov D K, Landau D P, Lewyn L, Makarov D E, Margarida M Telo da Gama, Metropolis N, Micheletti C, Mirny L, Miyazawa S, Nelson E D, Pande V S, Patrícia F N Faísca, Plaxco K W, Plaxco K W, Prakash N, Rui D M Travasso, Sali A, Shakhnovich E I, Shakhnovich E I, Shakhnovich E I, Socci N D, Tiana G, Vendruscolo M, Wallin S, Wallin S, Wetlaufer D E, Zhou H   +45 more
arxiv   +3 more sources

Cooperativity and the origins of rapid, single-exponential kinetics in protein folding [PDF]

Protein Science 15, 1608-1618 (2006), 2006
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to the extraordinary thermodynamic cooperativity of protein
Abkevich, Abkevich, Bryngelson, Bryngelson, Bryngelson, Buchler, Chan, Chan, Chan, Cieplack, Cieplack, Cieplak, Eastwood, Ejtehadi, Fan, Faísca, Faísca, Faísca, Fernandez, Gillespie, Gillespie, Gillespie, Govindarajan, Gromiha, Gutin, Gutin, Gutin, Jewett, Kaya, Kaya, Kaya, Kaya, Kaya, Kevin W. Plaxco, Kuhlman, Landau, Makarov, Makhatadze, Metropolis, Miller, Mirny, Mirny, Miyazawa, Nelson, Nymeyer, Onuchic, Patrícia F.N. Faísca, Plaxco, Plaxco, Plotkin, Saitoh, Sali, Scalley-Kim, Shakhnovich, Shakhnovich, Shakhnovich, Shea, Shimizu, Socci, Takada, Wyman, Zhu   +61 more
arxiv   +4 more sources

Funnels, Pathways and the Energy Landscape of Protein Folding: A Synthesis [PDF]

Proteins-Struct. Func. and Genetics. 21 (1995) 167, 1994
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors,
J. Bryngelson, J. Onuchic, N. Socci, P. Wolynes   +3 more
arxiv   +3 more sources

Protein folding tames chaos [PDF]

arXiv, 2013
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to theoretical modeling and computer simulations.
Wei, Guo-Wei, Xia, Kelin
arxiv   +3 more sources

The evaluation of protein folding rate constant is improved by predicting the folding kinetic order with a SVM-based method [PDF]

arXiv, 2006
Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have been developed to predict the protein folding rate considering the relationships of the process with tolopological
Capriotti, Emidio, Casadio, Rita
arxiv   +2 more sources

ColabFold: making protein folding accessible to all

Nature Methods, 2022
ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold.
M. Mirdita, S. Ovchinnikov, Martin Steinegger   +2 more
semanticscholar   +1 more source

Protein structure generation via folding diffusion [PDF]

Nature Communications, 2022
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases.
Kevin E. Wu, Kevin Kaichuang Yang, Rianne van den Berg, James Zou, Alex X. Lu, Ava P. Amini   +5 more
semanticscholar   +1 more source

Protein disulfide-isomerase interacts with a substrate protein at all stages along its folding pathway [PDF]

, 2014
In contrast to molecular chaperones that couple protein folding to ATP hydrolysis, protein disulfide-isomerase (PDI) catalyzes protein folding coupled to formation of disulfide bonds (oxidative folding).
A Jansens, A Land, A Pirneskoski, A. Katrine Wallis, Alistair G. Irvine, AR Karala, AR Karala, AY Denisov, B van den Berg, B van den Berg, B van den Berg, CB Anfinsen, Claudia A. Blindauer, CPM van Mierlo, CPM van Mierlo, CW Gruber, DP Goldenberg, E van Anken, F Hatahet, G Kozlov, G Wagner, HC Shin, HC Shin, J Riemer, JH Laity, JL Arolas, JS Weissman, JS Weissman, L Wang, LJ Byrne, Lloyd W. Ruddock, M Narayan, Mark J. Howard, Michelle L. Rowe, Narinder Sanghera, NJ Bulleid, NJ Darby, P Klappa, P Venetianer, RA Williamson, RB Freedman, RF Goldberger, Richard A. Williamson, RJ Ellis, Robert B. Freedman, S Masui, S Talluri, Salvador Ventura, TE Creighton, TE Creighton, TE Creighton, TE Creighton, VD Nguyen, VD Nguyen, WF Vranken   +54 more
core   +10 more sources