Results 21 to 30 of about 1,677,396 (366)

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.
Ya Jia, Yang Zhang, Haiyou Deng
openaire   +4 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

TMbed: transmembrane proteins predicted through language model embeddings

BMC Bioinformatics, 2022
Background Despite the immense importance of transmembrane proteins (TMP) for molecular biology and medicine, experimental 3D structures for TMPs remain about 4–5 times underrepresented compared to non-TMPs.
Michael Bernhofer, Burkhard Rost
doaj   +1 more source

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

BMC Bioinformatics, 2021
Background Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction.
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng   +3 more
doaj   +1 more source

Integrated structure-based protein interface prediction

BMC Bioinformatics, 2022
Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents.
M. Walder, E. Edelstein, M. Carroll, S. Lazarev, J. E. Fajardo, A. Fiser, R. Viswanathan   +6 more
doaj   +1 more source

Computational Approach for Protein Structure Prediction [PDF]

Healthcare Informatics Research, 2013
ObjectivesTo predict the structure of protein, which dictates the function it performs, a newly designed algorithm is developed which blends the concept of self-organization and the genetic algorithm.MethodsAmong many other approaches, genetic algorithm ...
Amouda Venkatesan, Jeyakodi Gopal, Manimozhi Candavelou, Sowjanya Gollapalli, Kayathri Karthikeyan   +4 more
doaj   +1 more source

A method for multiple-sequence-alignment-free protein structure prediction using a protein language model [PDF]

Nature Machine Intelligence, 2022
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on multiple sequence alignments (MSAs) as inputs to learn the co-evolution ...
Xiaomin Fang, Fan Wang, Lihang Liu, Jingzhou He, Dayong Lin, Yingfei Xiang, Xiaonan Zhang, Hua-Hong Wu, Hui Li, Le Song   +9 more
semanticscholar   +1 more source

Water in protein structure prediction [PDF]

Proceedings of the National Academy of Sciences, 2004
Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins.
Garegin A. Papoian, Johan Ulander, Johan Ulander, Zaida Luthey-Schulten, Michael P. Eastwood, Michael P. Eastwood, Peter G. Wolynes   +6 more
openaire   +4 more sources

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

bioRxiv, 2023
Designing proteins to achieve specific functions often requires in silico modeling of their properties at high throughput scale and can significantly benefit from fast and accurate protein structure prediction.
Jae Hyeon Lee, Payman Yadollahpour, A. Watkins, Nathan C Frey, Andrew Leaver-Fay, Stephen Ra, Kyunghyun Cho, V. Gligorijević, A. Regev, Richard Bonneau   +9 more
semanticscholar   +1 more source