Zobrazeno 1 - 10
of 88
pro vyhledávání: '"Genki Terashi"'
Autor:
Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, Daisuke Kihara
Publikováno v:
Communications Biology, Vol 5, Iss 1, Pp 1-12 (2022)
3D-AF-Surfer is presented as a computational resource for real-time protein structure comparison search between AlphaFold2 models and PDB entries within seconds to a few minutes.
Externí odkaz:
https://doaj.org/article/8610575ad26f4db68e608b509adf74b2
Publikováno v:
Frontiers in Molecular Biosciences, Vol 9 (2022)
An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual struc
Externí odkaz:
https://doaj.org/article/22cba81fae8148c991e6e85f482ca476
Autor:
Xiao Wang, Eman Alnabati, Tunde W. Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Genki Terashi, Daisuke Kihara
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-9 (2021)
It is challenging to extract structural information from EM density maps at intermediate or low resolutions. Here, the authors present Emap2sec+, a program for detecting nucleotides and protein secondary structures in EM density maps at 5 to 10 Å re
Externí odkaz:
https://doaj.org/article/7fdf26b480c34d9188c773c5752a3afa
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)
Here, the authors present VESPER, a program for EM density map search and alignment. Using benchmark datasets, they demonstrate that VESPER performs accurate global and local alignments and comparisons of EM maps.
Externí odkaz:
https://doaj.org/article/80c1de7ec4114f6c9d64b4218118b846
Autor:
Aashish Jain, Genki Terashi, Yuki Kagaya, Sai Raghavendra Maddhuri Venkata Subramaniya, Charles Christoffer, Daisuke Kihara
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
Abstract Protein 3D structure prediction has advanced significantly in recent years due to improving contact prediction accuracy. This improvement has been largely due to deep learning approaches that predict inter-residue contacts and, more recently
Externí odkaz:
https://doaj.org/article/4b802a2160964401b3d88deddd0fef82
Autor:
Genki Terashi, Daisuke Kihara
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-11 (2018)
Main-chain tracing remains a time-consuming task for medium resolution cryo-EM maps. Here the authors describe MAINMAST, a computational approach for building main-chain structure models of proteins from EM maps of 4-5 Å resolution that builds main-
Externí odkaz:
https://doaj.org/article/ab319603714d4b1b8150b89930cce550
Autor:
Lenna X Peterson, Yoichiro Togawa, Juan Esquivel-Rodriguez, Genki Terashi, Charles Christoffer, Amitava Roy, Woong-Hee Shin, Daisuke Kihara
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 1, p e1005937 (2018)
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine
Externí odkaz:
https://doaj.org/article/16b06e1513864f2d98752550f36a8349
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 4, p e1005485 (2017)
Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant stru
Externí odkaz:
https://doaj.org/article/3cf5f1d94cc04c2db175e95c3f04636f
Autor:
Genki Terashi, Mayuko Takeda-Shitaka
Publikováno v:
PLoS ONE, Vol 10, Iss 10, p e0141440 (2015)
Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein s
Externí odkaz:
https://doaj.org/article/8860c0c6d44147ed83ef41d152180180
Autor:
Harrison Helmick, Anika Jain, Genki Terashi, Andrea Liceaga, Arun K. Bhunia, Daisuke Kihara, Jozef L. Kokini
Publikováno v:
Annual Review of Food Science and Technology. 14:203-224
Structural bioinformatics analyzes protein structural models with the goal of uncovering molecular drivers of food functionality. This field aims to develop tools that can rapidly extract relevant information from protein databases as well as organiz
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::acfc7822c5a3e2f81449b431ba47f5e8
https://doi.org/10.1146/annurev-food-060721-022222
https://doi.org/10.1146/annurev-food-060721-022222