MAINMAST: de novo protein structure modeling for cryo-EM maps assisted by structure feature detection by deep learning

3P268 De Novo protein structure modeling by rewiring old folds(20. Origin of life & Evolution,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s293_4 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S293

Author(s):

Shunsuke Nishiyama ◽

Tatsuo Mukai ◽

George Chikenji

Keyword(s):

Protein Structure ◽

Annual Meeting ◽

Origin Of Life ◽

De Novo ◽

Structure Modeling ◽

Biophysical Society

Deep learning and protein structure modeling

Nature Methods ◽

10.1038/s41592-021-01360-8 ◽

2022 ◽

Vol 19 (1) ◽

pp. 13-14

Author(s):

Minkyung Baek ◽

David Baker

Keyword(s):

Deep Learning ◽

Protein Structure ◽

Structure Modeling ◽

De Novo Protein Structure Modeling Tool MAINMAST Enhanced for Multiple Chain Complexes and Bound Ligands

Biophysical Journal ◽

10.1016/j.bpj.2019.11.2667 ◽

2020 ◽

Vol 118 (3) ◽

pp. 481a

Author(s):

Genki Terashi ◽

Daisuke Kihara

Keyword(s):

Protein Structure ◽

De Novo ◽

Structure Modeling ◽

Modeling Tool ◽

Chain Complexes ◽

Multiple Chain

In silico Protein Structure Modeling and Conservation Analysis of ChrR, a Class-I Chromate Reducing Flavoenzyme from Pseudomonas putida

Protein and Peptide Letters ◽

10.2174/0929866511320090011 ◽

2013 ◽

Vol 20 (9) ◽

pp. 1049-1053 ◽

Cited By ~ 2

Author(s):

Shivani Viradia ◽

Anjana Vala

Keyword(s):

Protein Structure ◽

Pseudomonas Putida ◽

In Silico ◽

Class I ◽

Structure Modeling ◽

Conservation Analysis ◽

ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and H β protons

Journal of Computational Chemistry ◽

10.1002/jcc.26695 ◽

2021 ◽

Author(s):

Emilia A. Lubecka ◽

Adam Liwo

Keyword(s):

Nuclear Magnetic Resonance ◽

Protein Structure ◽

Magnetic Resonance ◽

Coarse Grained ◽

Structure Modeling ◽

Analytical Estimation ◽

Atomic Coordinates ◽

Nuclear Magnetic

Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments

Bioinformatics ◽

10.1093/bioinformatics/btm377 ◽

2007 ◽

Vol 23 (19) ◽

pp. 2558-2565 ◽

Cited By ~ 66

Author(s):

N. Fernandez-Fuentes ◽

B. K. Rai ◽

C. J. Madrid-Aliste ◽

J. Eduardo Fajardo ◽

A. Fiser

Keyword(s):

Protein Structure ◽

Structure Modeling ◽

Multiple Templates

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

Nucleic Acids Research ◽

10.1093/nar/gkq369 ◽

2010 ◽

Vol 38 (Web Server) ◽

pp. W569-W575 ◽

Cited By ~ 80

Author(s):

F. Lauck ◽

C. A. Smith ◽

G. F. Friedland ◽

E. L. Humphris ◽

T. Kortemme

Keyword(s):

Protein Structure ◽

Web Server ◽

Structure Modeling ◽

Evaluation of comparative protein structure modeling by MODELLER-3

Proteins Structure Function and Bioinformatics ◽

10.1002/(sici)1097-0134(1997)1+<50::aid-prot8>3.0.co;2-s ◽

1997 ◽

Vol 29 (S1) ◽

pp. 50-58 ◽

Cited By ~ 153

Author(s):

Roberto Sánchez ◽

Andrej Šali

Keyword(s):

Protein Structure ◽

Structure Modeling ◽

AS2TS system for protein structure modeling and analysis

Nucleic Acids Research ◽

10.1093/nar/gki457 ◽

2005 ◽

Vol 33 (Web Server) ◽

pp. W111-W115 ◽

Cited By ~ 31

Author(s):

A. Zemla ◽

C. E. Zhou ◽

T. Slezak ◽

T. Kuczmarski ◽

D. Rama ◽

...

Keyword(s):

Protein Structure ◽

Structure Modeling ◽

Modeling And Analysis ◽

NATO Science for Peace and Security Series A: Chemistry and Biology - From Molecules to Medicines ◽

Protein Structure Modeling

10.1007/978-90-481-2339-1_9 ◽

2009 ◽

pp. 139-151 ◽

Cited By ~ 2

Author(s):

Narayanan Eswar ◽

Andrej Sali

Keyword(s):

Protein Structure ◽

Structure Modeling ◽