A citation-based method for searching scientific literature

Douglas E V Pires, David B Ascher, Tom L Blundell. Nucleic Acids Res 2014
Times Cited: 396







List of co-cited articles
551 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
453
52

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
369
46

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
230
37

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
935
32

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


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
288
19

CUPSAT: prediction of protein stability upon point mutations.
Vijaya Parthiban, M Michael Gromiha, Dietmar Schomburg. Nucleic Acids Res 2006
375
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
298
19

MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
127
16

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
14

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
82
17

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
60
23


MAESTROweb: a web server for structure-based protein stability prediction.
Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner. Bioinformatics 2016
66
19

mCSM-membrane: predicting the effects of mutations on transmembrane proteins.
Douglas E V Pires, Carlos H M Rodrigues, David B Ascher. Nucleic Acids Res 2020
22
54

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.
Carlos H M Rodrigues, Yoochan Myung, Douglas E V Pires, David B Ascher. Nucleic Acids Res 2019
106
12

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
90
12

A three-state prediction of single point mutations on protein stability changes.
Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio. BMC Bioinformatics 2008
215
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
256
10

Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
55
18

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2017
62
16

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
261
10


SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
9


DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations.
Carlos H M Rodrigues, Douglas E V Pires, David B Ascher. Protein Sci 2021
46
19

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
34
26

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
9

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
90
10

MutationTaster2: mutation prediction for the deep-sequencing age.
Jana Marie Schwarz, David N Cooper, Markus Schuelke, Dominik Seelow. Nat Methods 2014
8



Predicting functional effect of human missense mutations using PolyPhen-2.
Ivan Adzhubei, Daniel M Jordan, Shamil R Sunyaev. Curr Protoc Hum Genet 2013
8

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations.
Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli. BMC Bioinformatics 2019
25
32


CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
72
11

Systematic Investigation of the Data Set Dependency of Protein Stability Predictors.
Octav Caldararu, Rukmankesh Mehra, Tom L Blundell, Kasper P Kepp. J Chem Inf Model 2020
15
53

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
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
83
8

Stability effects of mutations and protein evolvability.
Nobuhiko Tokuriki, Dan S Tawfik. Curr Opin Struct Biol 2009
445
7


Performance of protein stability predictors.
Sofia Khan, Mauno Vihinen. Hum Mutat 2010
206
7

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
143
7

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
7

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
374
7


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
7

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures.
Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell. J Mol Biol 2017
177
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.