Results 11 to 20 of about 1,386,650 (240)

Protein structure prediction has reached the single-structure frontier. [PDF]

Nat Methods, 2023
Dramatic advances in protein structure prediction have sparked debate as to whether the problem of predicting structure from sequence is solved or not. Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a
Lane TJ.
europepmc   +2 more sources

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. [PDF]

Nat Biotechnol, 2023
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the
Stahl K, Graziadei A, Dau T, Brock O, Rappsilber J.   +4 more
europepmc   +2 more sources

Phyre2.2: A Community Resource for Template-based Protein Structure Prediction. [PDF]

J Mol Biol
Powell HR, Islam SA, David A, Sternberg MJE.   +3 more
europepmc   +2 more sources

Protein Structure Prediction [PDF]

Biophysical Journal, 2008
Protein structure prediction has matured over the past few years to the point that even fully automated methods can provide reasonably accurate three-dimensional models of protein structures. However, until now it has not been possible to develop programs able to perform as well as human experts, who are still capable of systematically producing better
AlLazikani B, Hill EE, Morea V
  +11 more sources

Single-sequence protein structure prediction using a language model and deep learning. [PDF]

Nat Biotechnol, 2022
Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M.   +11 more
europepmc   +2 more sources

Deep template-based protein structure prediction.

PLoS Computational Biology, 2021
MotivationProtein structure prediction has been greatly improved by deep learning, but most efforts are devoted to template-free modeling. But very few deep learning methods are developed for TBM (template-based modeling), a popular technique for protein
Fandi Wu, Jinbo Xu
doaj   +1 more source

Evolutionary-scale prediction of atomic level protein structure with a language model

bioRxiv, 2022
Artificial intelligence has the potential to open insight into the structure of proteins at the scale of evolution. It has only recently been possible to extend protein structure prediction to two hundred million cataloged proteins.
Zeming Lin, Halil Akin, Roshan Rao, Brian L. Hie, Zhongkai Zhu, Wenting Lu, Nikita Smetanin, Robert Verkuil, Ori Kabeli, Y. Shmueli, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Salvatore Candido, Alexander Rives   +14 more
semanticscholar   +1 more source

Protein structure prediction [PDF]

International Journal of Modern Physics B, 2018
Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction.
Haiyou, Deng, Ya, Jia, Yang, Zhang
openaire   +3 more sources

Highly accurate protein structure prediction for the human proteome

Nature, 2021
Protein structures can provide invaluable information, both for reasoning about biological processes and for enabling interventions such as structure-based drug development or targeted mutagenesis.
Kathryn Tunyasuvunakool, J. Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, A. Cowie, Clemens Meyer, Agata Laydon, S. Velankar, G. Kleywegt, A. Bateman, R. Evans, A. Pritzel, Michael Figurnov, O. Ronneberger, Russ Bates, Simon A A Kohl, Anna Potapenko, A. J. Ballard, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Ellen Clancy, D. Reiman, Stig Petersen, A. Senior, K. Kavukcuoglu, E. Birney, Pushmeet Kohli, J. Jumper, D. Hassabis   +32 more
semanticscholar   +1 more source

How long is a piece of loop? [PDF]

PeerJ, 2013
Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict.
Yoonjoo Choi, Sumeet Agarwal, Charlotte M. Deane   +2 more
doaj   +2 more sources