Hua Cheng, R Dustin Schaeffer, Yuxing Liao, Lisa N Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V Grishin. PLoS Comput Biol 2014
Times Cited: 158
Times Cited: 158
Times Cited
Times Co-cited
Similarity
SCOP: a structural classification of proteins database for the investigation of sequences and structures.
A G Murzin, S E Brenner, T Hubbard, C Chothia. J Mol Biol 1995
A G Murzin, S E Brenner, T Hubbard, C Chothia. J Mol Biol 1995
24
The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
23
TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
22
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
21
CATH: an expanded resource to predict protein function through structure and sequence.
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo, Ian Sillitoe. Nucleic Acids Res 2017
Natalie L Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, David Lee, Paul Ashford, Christine A Orengo, Ian Sillitoe. Nucleic Acids Res 2017
21
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures.
Naomi K Fox, Steven E Brenner, John-Marc Chandonia. Nucleic Acids Res 2014
Naomi K Fox, Steven E Brenner, John-Marc Chandonia. Nucleic Acids Res 2014
20
A vocabulary of ancient peptides at the origin of folded proteins.
Vikram Alva, Johannes Söding, Andrei N Lupas. Elife 2015
Vikram Alva, Johannes Söding, Andrei N Lupas. Elife 2015
19
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
17
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
W Kabsch, C Sander. Biopolymers 1983
W Kabsch, C Sander. Biopolymers 1983
16
Manual classification strategies in the ECOD database.
Hua Cheng, Yuxing Liao, R Dustin Schaeffer, Nick V Grishin. Proteins 2015
Hua Cheng, Yuxing Liao, R Dustin Schaeffer, Nick V Grishin. Proteins 2015
50
On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
A N Lupas, C P Ponting, R B Russell. J Struct Biol 2001
A N Lupas, C P Ponting, R B Russell. J Struct Biol 2001
13
Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2017
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2017
39
CATH--a hierarchic classification of protein domain structures.
C A Orengo, A D Michie, S Jones, D T Jones, M B Swindells, J M Thornton. Structure 1997
C A Orengo, A D Michie, S Jones, D T Jones, M B Swindells, J M Thornton. Structure 1997
12
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.
Antonina Andreeva, Eugene Kulesha, Julian Gough, Alexey G Murzin. Nucleic Acids Res 2020
Antonina Andreeva, Eugene Kulesha, Julian Gough, Alexey G Murzin. Nucleic Acids Res 2020
19
A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva. J Mol Biol 2018
Lukas Zimmermann, Andrew Stephens, Seung-Zin Nam, David Rau, Jonas Kübler, Marko Lozajic, Felix Gabler, Johannes Söding, Andrei N Lupas, Vikram Alva. J Mol Biol 2018
11
Evolution of the structure of ferredoxin based on living relics of primitive amino Acid sequences.
R V Eck, M O Dayhoff. Science 1966
R V Eck, M O Dayhoff. Science 1966
11
Simple yet functional phosphate-loop proteins.
Maria Luisa Romero Romero, Fan Yang, Yu-Ru Lin, Agnes Toth-Petroczy, Igor N Berezovsky, Alexander Goncearenco, Wen Yang, Alon Wellner, Fanindra Kumar-Deshmukh, Michal Sharon,[...]. Proc Natl Acad Sci U S A 2018
Maria Luisa Romero Romero, Fan Yang, Yu-Ru Lin, Agnes Toth-Petroczy, Igor N Berezovsky, Alexander Goncearenco, Wen Yang, Alon Wellner, Fanindra Kumar-Deshmukh, Michal Sharon,[...]. Proc Natl Acad Sci U S A 2018
32
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10
Protein secondary structure prediction based on position-specific scoring matrices.
D T Jones. J Mol Biol 1999
D T Jones. J Mol Biol 1999
10
ECOD: new developments in the evolutionary classification of domains.
R Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V Grishin. Nucleic Acids Res 2017
R Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V Grishin. Nucleic Acids Res 2017
32
An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.
Paola Laurino, Ágnes Tóth-Petróczy, Rubén Meana-Pañeda, Wei Lin, Donald G Truhlar, Dan S Tawfik. PLoS Biol 2016
Paola Laurino, Ágnes Tóth-Petróczy, Rubén Meana-Pañeda, Wei Lin, Donald G Truhlar, Dan S Tawfik. PLoS Biol 2016
20
The Pfam protein families database in 2019.
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
Sara El-Gebali, Jaina Mistry, Alex Bateman, Sean R Eddy, Aurélien Luciani, Simon C Potter, Matloob Qureshi, Lorna J Richardson, Gustavo A Salazar, Alfredo Smart,[...]. Nucleic Acids Res 2019
10
Improved protein structure prediction using potentials from deep learning.
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Nature 2020
10
Protein structure determination using metagenome sequence data.
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker. Science 2017
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker. Science 2017
9
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database.
John-Marc Chandonia, Naomi K Fox, Steven E Brenner. J Mol Biol 2017
John-Marc Chandonia, Naomi K Fox, Steven E Brenner. J Mol Biol 2017
17
Global view of the protein universe.
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2014
Sergey Nepomnyachiy, Nir Ben-Tal, Rachel Kolodny. Proc Natl Acad Sci U S A 2014
20
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.
E Krissinel, K Henrick. Acta Crystallogr D Biol Crystallogr 2004
E Krissinel, K Henrick. Acta Crystallogr D Biol Crystallogr 2004
9
A galaxy of folds.
Vikram Alva, Michael Remmert, Andreas Biegert, Andrei N Lupas, Johannes Söding. Protein Sci 2010
Vikram Alva, Michael Remmert, Andreas Biegert, Andrei N Lupas, Johannes Söding. Protein Sci 2010
17
HH-suite3 for fast remote homology detection and deep protein annotation.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J Haunsberger, Johannes Söding. BMC Bioinformatics 2019
9
Scoring function for automated assessment of protein structure template quality.
Yang Zhang, Jeffrey Skolnick. Proteins 2004
Yang Zhang, Jeffrey Skolnick. Proteins 2004
8
How significant is a protein structure similarity with TM-score = 0.5?
Jinrui Xu, Yang Zhang. Bioinformatics 2010
Jinrui Xu, Yang Zhang. Bioinformatics 2010
8
Comparative protein modelling by satisfaction of spatial restraints.
A Sali, T L Blundell. J Mol Biol 1993
A Sali, T L Blundell. J Mol Biol 1993
8
Evolutionary relationship of two ancient protein superfolds.
José Arcadio Farías-Rico, Steffen Schmidt, Birte Höcker. Nat Chem Biol 2014
José Arcadio Farías-Rico, Steffen Schmidt, Birte Höcker. Nat Chem Biol 2014
20
SCOP2 prototype: a new approach to protein structure mining.
Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G Murzin. Nucleic Acids Res 2014
Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G Murzin. Nucleic Acids Res 2014
8
More than the sum of their parts: on the evolution of proteins from peptides.
Johannes Söding, Andrei N Lupas. Bioessays 2003
Johannes Söding, Andrei N Lupas. Bioessays 2003
8
The Pfam protein families database: towards a more sustainable future.
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
Robert D Finn, Penelope Coggill, Ruth Y Eberhardt, Sean R Eddy, Jaina Mistry, Alex L Mitchell, Simon C Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas,[...]. Nucleic Acids Res 2016
8
The HHpred interactive server for protein homology detection and structure prediction.
Johannes Söding, Andreas Biegert, Andrei N Lupas. Nucleic Acids Res 2005
Johannes Söding, Andreas Biegert, Andrei N Lupas. Nucleic Acids Res 2005
7
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
Valerio Mariani, Marco Biasini, Alessandro Barbato, Torsten Schwede. Bioinformatics 2013
Valerio Mariani, Marco Biasini, Alessandro Barbato, Torsten Schwede. Bioinformatics 2013
7
7
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
I N Shindyalov, P E Bourne. Protein Eng 1998
I N Shindyalov, P E Bourne. Protein Eng 1998
7
Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
7
CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Ian Sillitoe, Natalie Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, Paul Ashford, Adeyelu Tolulope, Harry M Scholes, Ilya Senatorov, Andra Bujan,[...]. Nucleic Acids Res 2019
Ian Sillitoe, Natalie Dawson, Tony E Lewis, Sayoni Das, Jonathan G Lees, Paul Ashford, Adeyelu Tolulope, Harry M Scholes, Ilya Senatorov, Andra Bujan,[...]. Nucleic Acids Res 2019
10
Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
7
Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
7
CASP11 statistics and the prediction center evaluation system.
Andriy Kryshtafovych, Bohdan Monastyrskyy, Krzysztof Fidelis. Proteins 2016
Andriy Kryshtafovych, Bohdan Monastyrskyy, Krzysztof Fidelis. Proteins 2016
20
Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.