A citation-based method for searching scientific literature

Jinrui Xu, Yang Zhang. Bioinformatics 2010
Times Cited: 404







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



Times Cited
  Times     Co-cited
Similarity



TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
47

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
428
35

The I-TASSER Suite: protein structure and function prediction.
Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang. Nat Methods 2015
27

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
716
26

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
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
403
24

Critical assessment of methods of protein structure prediction (CASP)-Round XIII.
Andriy Kryshtafovych, Torsten Schwede, Maya Topf, Krzysztof Fidelis, John Moult. Proteins 2019
181
20

Distance-based protein folding powered by deep learning.
Jinbo Xu. Proc Natl Acad Sci U S A 2019
156
20

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
18


Protein homology detection by HMM-HMM comparison.
Johannes Söding. Bioinformatics 2005
15


ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks.
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, Yang Zhang. Bioinformatics 2019
73
20

Deep-learning contact-map guided protein structure prediction in CASP13.
Wei Zheng, Yang Li, Chengxin Zhang, Robin Pearce, S M Mortuza, Yang Zhang. Proteins 2019
88
17

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Michael Remmert, Andreas Biegert, Andreas Hauser, Johannes Söding. Nat Methods 2011
15


SPICKER: a clustering approach to identify near-native protein folds.
Yang Zhang, Jeffrey Skolnick. J Comput Chem 2004
261
13

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
12

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
171
12

Critical assessment of methods of protein structure prediction (CASP)-Round XII.
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Anna Tramontano. Proteins 2018
168
12

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
11



Clustering huge protein sequence sets in linear time.
Martin Steinegger, Johannes Söding. Nat Commun 2018
155
11




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
270
10


PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments.
David T Jones, Daniel W A Buchan, Domenico Cozzetto, Massimiliano Pontil. Bioinformatics 2012
456
10





Protein structure prediction and analysis using the Robetta server.
David E Kim, Dylan Chivian, David Baker. Nucleic Acids Res 2004
9

CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.
Stefan Seemayer, Markus Gruber, Johannes Söding. Bioinformatics 2014
214
9

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
438
9

The Phyre2 web portal for protein modeling, prediction and analysis.
Lawrence A Kelley, Stefans Mezulis, Christopher M Yates, Mark N Wass, Michael J E Sternberg. Nat Protoc 2015
8

Template-based protein structure modeling using the RaptorX web server.
Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu, Jinbo Xu. Nat Protoc 2012
964
8

LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins.
Wei Zheng, Chengxin Zhang, Qiqige Wuyun, Robin Pearce, Yang Li, Yang Zhang. Nucleic Acids Res 2019
59
13

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13).
Andrew W Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W R Nelson, Alex Bridgland,[...]. Proteins 2019
108
8

Protein structure prediction using Rosetta.
Carol A Rohl, Charlie E M Strauss, Kira M S Misura, David Baker. Methods Enzymol 2004
964
8


NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers.
Baoji He, S M Mortuza, Yanting Wang, Hong-Bin Shen, Yang Zhang. Bioinformatics 2017
40
20

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.
Hetunandan Kamisetty, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2013
375
8


Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
7

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
7

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Anna Tramontano. Proteins 2016
127
7


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.