A citation-based method for searching scientific literature

Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
Times Cited: 803







List of co-cited articles
527 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
378
24


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
20

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
238
20

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
18


SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
16

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
176
15

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
15

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
14


Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
14

CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
335
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
962
12

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
260
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
898
12

A three-state prediction of single point mutations on protein stability changes.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio. BMC Bioinformatics 2008
197
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
433
11

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
269
11

MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
106
11

SNAP: predict effect of non-synonymous polymorphisms on function.
Yana Bromberg, Burkhard Rost. Nucleic Acids Res 2007
512
10

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
310
10

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
10

iStable: off-the-shelf predictor integration for predicting protein stability changes.
Chi-Wei Chen, Jerome Lin, Yen-Wei Chu. BMC Bioinformatics 2013
90
11

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

Functional annotations improve the predictive score of human disease-related mutations in proteins.
Remo Calabrese, Emidio Capriotti, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. Hum Mutat 2009
342
9


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
9

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
9

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
223
8

Better prediction of functional effects for sequence variants.
Maximilian Hecht, Yana Bromberg, Burkhard Rost. BMC Genomics 2015
199
8

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
58
13


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
113
8

Collective judgment predicts disease-associated single nucleotide variants.
Emidio Capriotti, Russ B Altman, Yana Bromberg. BMC Genomics 2013
125
8

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks.
Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z Zhang. J Chem Inf Model 2019
32
25

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
M D Shaji Kumar, K Abdulla Bava, M Michael Gromiha, Ponraj Prabakaran, Koji Kitajima, Hatsuho Uedaira, Akinori Sarai. Nucleic Acids Res 2006
248
8


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
810
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
223
8

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Bette Korber, Will M Fischer, Sandrasegaram Gnanakaran, Hyejin Yoon, James Theiler, Werner Abfalterer, Nick Hengartner, Elena E Giorgi, Tanmoy Bhattacharya, Brian Foley,[...]. Cell 2020
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
77
9

Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
37
18


GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
7


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
56
12

Performance of protein stability predictors.
Sofia Khan, Mauno Vihinen. Hum Mutat 2010
191
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.