A citation-based method for searching scientific literature

Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, Ivan Anishchenko, Justas Dauparas, David Baker. Nat Commun 2021
Times Cited: 44







List of co-cited articles
336 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
387
63

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
667
45

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
38

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
147
36


Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
314
27

Distance-based protein folding powered by deep learning.
Jinbo Xu. Proc Natl Acad Sci U S A 2019
150
25

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. PLoS Comput Biol 2017
386
18

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning.
Jonghun Won, Minkyung Baek, Bohdan Monastyrskyy, Andriy Kryshtafovych, Chaok Seok. Proteins 2019
26
30

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
18

Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
173
18


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
178
18

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
18

ProQ3D: improved model quality assessments using deep learning.
Karolis Uziela, David Menéndez Hurtado, Nanjiang Shu, Björn Wallner, Arne Elofsson. Bioinformatics 2017
78
15

TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
15


Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J Martin, Johannes Söding, Martin Steinegger. Nucleic Acids Res 2017
153
15


PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.
Sidhartha Chaudhury, Sergey Lyskov, Jeffrey J Gray. Bioinformatics 2010
280
15

Protein model quality assessment using 3D oriented convolutional neural networks.
Guillaume Pagès, Benoit Charmettant, Sergei Grudinin. Bioinformatics 2019
25
24

Smooth orientation-dependent scoring function for coarse-grained protein quality assessment.
Mikhail Karasikov, Guillaume Pagès, Sergei Grudinin. Bioinformatics 2019
31
19


QAcon: single model quality assessment using protein structural and contact information with machine learning techniques.
Renzhi Cao, Badri Adhikari, Debswapna Bhattacharya, Miao Sun, Jie Hou, Jianlin Cheng. Bioinformatics 2017
55
13


Estimation of model accuracy in CASP13.
Jianlin Cheng, Myong-Ho Choe, Arne Elofsson, Kun-Sop Han, Jie Hou, Ali H A Maghrabi, Liam J McGuffin, David Menéndez-Hurtado, Kliment Olechnovič, Torsten Schwede,[...]. Proteins 2019
31
19

Evaluation of model refinement in CASP13.
Randy J Read, Massimo D Sammito, Andriy Kryshtafovych, Tristan I Croll. Proteins 2019
21
28

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
13


Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.
Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C Lawrence Zitnick, Jerry Ma,[...]. Proc Natl Acad Sci U S A 2021
98
13

GraphQA: protein model quality assessment using graph convolutional networks.
Federico Baldassarre, David Menéndez Hurtado, Arne Elofsson, Hossein Azizpour. Bioinformatics 2021
14
42

Highly accurate protein structure prediction for the human proteome.
Kathryn Tunyasuvunakool, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, Andrew Cowie, Clemens Meyer, Agata Laydon,[...]. Nature 2021
262
13

VoroCNN: Deep convolutional neural network built on 3D Voronoi tessellation of protein structures.
Ilia Igashov, Liment Olechnovič, Maria Kadukova, Česlovas Venclovas, Sergei Grudinin. Bioinformatics 2021
7
71

High-accuracy refinement using Rosetta in CASP13.
Hahnbeom Park, Gyu Rie Lee, David E Kim, Ivan Anishchenko, Qian Cong, David Baker. Proteins 2019
20
25

VoroMQA: Assessment of protein structure quality using interatomic contact areas.
Kliment Olechnovič, Česlovas Venclovas. Proteins 2017
64
11

Assessment of model accuracy estimations in CASP12.
Andriy Kryshtafovych, Bohdan Monastyrskyy, Krzysztof Fidelis, Torsten Schwede, Anna Tramontano. Proteins 2018
35
14

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure.
Gyu Rie Lee, Jonghun Won, Lim Heo, Chaok Seok. Nucleic Acids Res 2019
25
20

Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
11


DeepDist: real-value inter-residue distance prediction with deep residual convolutional network.
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng. BMC Bioinformatics 2021
21
23

Protein structure prediction using Rosetta.
Carol A Rohl, Charlie E M Strauss, Kira M S Misura, David Baker. Methods Enzymol 2004
959
11


High-resolution comparative modeling with RosettaCM.
Yifan Song, Frank DiMaio, Ray Yu-Ruei Wang, David Kim, Chris Miles, Tj Brunette, James Thompson, David Baker. Structure 2013
569
11

Relaxation of backbone bond geometry improves protein energy landscape modeling.
Patrick Conway, Michael D Tyka, Frank DiMaio, David E Konerding, David Baker. Protein Sci 2014
167
11

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.
P Gainza, F Sverrisson, F Monti, E Rodolà, D Boscaini, M M Bronstein, B E Correia. Nat Methods 2020
78
11


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
9



GalaxyRefine: Protein structure refinement driven by side-chain repacking.
Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res 2013
321
9


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.