A citation-based method for searching scientific literature

Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
Times Cited: 386







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



Times Cited
  Times     Co-cited
Similarity


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
35

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
34


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
28


SDM: a server for predicting effects of mutations on protein stability.
Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B Ascher, Tom L Blundell. Nucleic Acids Res 2017
244
27

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.
Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis, Marianne Rooman. BMC Bioinformatics 2011
295
23

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
23


The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
19

SDM--a server for predicting effects of mutations on protein stability and malfunction.
Catherine L Worth, Robert Preissner, Tom L Blundell. Nucleic Acids Res 2011
306
15


MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
131
14

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
13

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
14

Predicting the functional impact of protein mutations: application to cancer genomics.
Boris Reva, Yevgeniy Antipin, Chris Sander. Nucleic Acids Res 2011
12

INPS-MD: a web server to predict stability of protein variants from sequence and structure.
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. Bioinformatics 2016
88
13


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
12

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
12



SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
11

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.
Yves Dehouck, Aline Grosfils, Benjamin Folch, Dimitri Gilis, Philippe Bogaerts, Marianne Rooman. Bioinformatics 2009
261
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
11

Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
11

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi,[...]. Am J Hum Genet 2016
784
11

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
11

A three-state prediction of single point mutations on protein stability changes.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio. BMC Bioinformatics 2008
221
11

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.
Hanka Venselaar, Tim A H Te Beek, Remko K P Kuipers, Maarten L Hekkelman, Gert Vriend. BMC Bioinformatics 2010
533
10

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
10

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Hashem A Shihab, Julian Gough, David N Cooper, Peter D Stenson, Gary L A Barker, Keith J Edwards, Ian N M Day, Tom R Gaunt. Hum Mutat 2013
716
10

MAESTROweb: a web server for structure-based protein stability prediction.
Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner. Bioinformatics 2016
69
14

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
10


iStable: off-the-shelf predictor integration for predicting protein stability changes.
Chi-Wei Chen, Jerome Lin, Yen-Wei Chu. BMC Bioinformatics 2013
109
9

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
9

Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine.
Tiziana Sanavia, Giovanni Birolo, Ludovica Montanucci, Paola Turina, Emidio Capriotti, Piero Fariselli. Comput Struct Biotechnol J 2020
40
22

Performance of protein stability predictors.
Sofia Khan, Mauno Vihinen. Hum Mutat 2010
210
8


ProTherm, version 4.0: thermodynamic database for proteins and mutants.
K Abdulla Bava, M Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai. Nucleic Acids Res 2004
245
8

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
8


ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.
Vincent Frappier, Matthieu Chartier, Rafael J Najmanovich. Nucleic Acids Res 2015
92
8

PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants.
Emidio Capriotti, Piero Fariselli. Nucleic Acids Res 2017
62
12

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
8

Better prediction of functional effects for sequence variants.
Maximilian Hecht, Yana Bromberg, Burkhard Rost. BMC Genomics 2015
264
8


SNAP: predict effect of non-synonymous polymorphisms on function.
Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
553
7

Collective judgment predicts disease-associated single nucleotide variants.
Emidio Capriotti, Russ B Altman, Yana Bromberg. BMC Genomics 2013
146
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.