A citation-based method for searching scientific literature

Hanka Venselaar, Tim A H Te Beek, Remko K P Kuipers, Maarten L Hekkelman, Gert Vriend. BMC Bioinformatics 2010
Times Cited: 533







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



Times Cited
  Times     Co-cited
Similarity


A method and server for predicting damaging missense mutations.
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
34


I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
976
27

SIFT web server: predicting effects of amino acid substitutions on proteins.
Ngak-Leng Sim, Prateek Kumar, Jing Hu, Steven Henikoff, Georg Schneider, Pauline C Ng. Nucleic Acids Res 2012
24

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
24

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
19



WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.
Emidio Capriotti, Remo Calabrese, Piero Fariselli, Pier Luigi Martelli, Russ B Altman, Rita Casadio. BMC Genomics 2013
158
15


Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
13

SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
13

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
12

Better prediction of functional effects for sequence variants.
Maximilian Hecht, Yana Bromberg, Burkhard Rost. BMC Genomics 2015
264
12


Predicting the functional effect of amino acid substitutions and indels.
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan. PLoS One 2012
12

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky. PLoS Comput Biol 2014
396
11

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability.
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
407
11

dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
10

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
10

TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
10

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update.
Víctor López-Ferrando, Andrea Gazzo, Xavier de la Cruz, Modesto Orozco, Josep Ll Gelpí. Nucleic Acids Res 2017
90
10

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley, Sylva L Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes,[...]. Nucleic Acids Res 2010
9

CADD: predicting the deleteriousness of variants throughout the human genome.
Philipp Rentzsch, Daniela Witten, Gregory M Cooper, Jay Shendure, Martin Kircher. Nucleic Acids Res 2019
8

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2.
Vikas Pejaver, Jorge Urresti, Jose Lugo-Martinez, Kymberleigh A Pagel, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N Cooper, Jonathan Sebat, Lilia M Iakoucheva,[...]. Nat Commun 2020
112
8



A general framework for estimating the relative pathogenicity of human genetic variants.
Martin Kircher, Daniela M Witten, Preti Jain, Brian J O'Roak, Gregory M Cooper, Jay Shendure. Nat Genet 2014
7

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.
Michael Schantz Klausen, Martin Closter Jespersen, Henrik Nielsen, Kamilla Kjaergaard Jensen, Vanessa Isabell Jurtz, Casper Kaae Sønderby, Morten Otto Alexander Sommer, Ole Winther, Morten Nielsen, Bent Petersen,[...]. Proteins 2019
197
7

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
7


ConSeq: the identification of functionally and structurally important residues in protein sequences.
Carine Berezin, Fabian Glaser, Josef Rosenberg, Inbal Paz, Tal Pupko, Piero Fariselli, Rita Casadio, Nir Ben-Tal. Bioinformatics 2004
344
7

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
Fabian Glaser, Tal Pupko, Inbal Paz, Rachel E Bell, Dalit Bechor-Shental, Eric Martz, Nir Ben-Tal. Bioinformatics 2003
863
6

CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
386
6

SNAP: predict effect of non-synonymous polymorphisms on function.
Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
553
6

mCSM: predicting the effects of mutations in proteins using graph-based signatures.
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
483
6


PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
Emidio Capriotti, Piero Fariselli. Nucleic Acids Res 2017
62
9

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk, Annika L Gable, David Lyon, Alexander Junge, Stefan Wyder, Jaime Huerta-Cepas, Milan Simonovic, Nadezhda T Doncheva, John H Morris, Peer Bork,[...]. Nucleic Acids Res 2019
6

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2010
6

Annotation of functional variation in personal genomes using RegulomeDB.
Alan P Boyle, Eurie L Hong, Manoj Hariharan, Yong Cheng, Marc A Schaub, Maya Kasowski, Konrad J Karczewski, Julie Park, Benjamin C Hitz, Shuai Weng,[...]. Genome Res 2012
6

The structural and functional signatures of proteins that undergo multiple events of post-translational modification.
Vikas Pejaver, Wei-Lun Hsu, Fuxiao Xin, A Keith Dunker, Vladimir N Uversky, Predrag Radivojac. Protein Sci 2014
230
6

Human non-synonymous SNPs: server and survey.
Vasily Ramensky, Peer Bork, Shamil Sunyaev. Nucleic Acids Res 2002
6

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
6

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
6

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
6

The InterPro protein families and domains database: 20 years on.
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj,[...]. Nucleic Acids Res 2021
484
6

Protein stability: a crystallographer's perspective.
Marc C Deller, Leopold Kong, Bernhard Rupp. Acta Crystallogr F Struct Biol Commun 2016
99
6

Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?
Sirawit Ittisoponpisan, Suhail A Islam, Tarun Khanna, Eman Alhuzimi, Alessia David, Michael J E Sternberg. J Mol Biol 2019
158
6



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.