Carlos H M Rodrigues, Douglas E V Pires, David B Ascher. Protein Sci 2021
Times Cited: 69
Times Cited: 69
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
Douglas E V Pires, David B Ascher, Tom L Blundell. Bioinformatics 2014
46
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.
Douglas E V Pires, David B Ascher, Tom L Blundell. Nucleic Acids Res 2014
Douglas E V Pires, David B Ascher, Tom L Blundell. Nucleic Acids Res 2014
37
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
Carlos Hm Rodrigues, Douglas Ev Pires, David B Ascher. Nucleic Acids Res 2018
34
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
Carlos H M Rodrigues, Yoochan Myung, Douglas E V Pires, David B Ascher. Nucleic Acids Res 2019
30
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
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
27
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
Arun Prasad Pandurangan, Bernardo Ochoa-Montaño, David B Ascher, Tom L Blundell. Nucleic Acids Res 2017
23
mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance.
Douglas E V Pires, Tom L Blundell, David B Ascher. Sci Rep 2016
Douglas E V Pires, Tom L Blundell, David B Ascher. Sci Rep 2016
18
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
Douglas E V Pires, Carlos H M Rodrigues, David B Ascher. Nucleic Acids Res 2020
40
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
Emidio Capriotti, Piero Fariselli, Rita Casadio. Nucleic Acids Res 2005
17
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2017
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2017
17
mmCSM-AB: guiding rational antibody engineering through multiple point mutations.
Yoochan Myung, Douglas E V Pires, David B Ascher. Nucleic Acids Res 2020
Yoochan Myung, Douglas E V Pires, David B Ascher. Nucleic Acids Res 2020
54
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
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
17
mCSM-AB2: guiding rational antibody design using graph-based signatures.
Yoochan Myung, Carlos H M Rodrigues, David B Ascher, Douglas E V Pires. Bioinformatics 2020
Yoochan Myung, Carlos H M Rodrigues, David B Ascher, Douglas E V Pires. Bioinformatics 2020
45
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
17
The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
15
CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
14
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
Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell. J Mol Biol 2017
13
mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria.
Douglas E V Pires, David B Ascher. J Chem Inf Model 2020
Douglas E V Pires, David B Ascher. J Chem Inf Model 2020
42
pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures.
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
Douglas E V Pires, Tom L Blundell, David B Ascher. J Med Chem 2015
13
ThermoMutDB: a thermodynamic database for missense mutations.
Joicymara S Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M Rezende, João P L Velloso, David B Ascher, Douglas E V Pires. Nucleic Acids Res 2021
Joicymara S Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M Rezende, João P L Velloso, David B Ascher, Douglas E V Pires. Nucleic Acids Res 2021
42
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels.
Yongwook Choi, Agnes P Chan. Bioinformatics 2015
Yongwook Choi, Agnes P Chan. Bioinformatics 2015
13
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
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
13
Prediction of protein stability changes for single-site mutations using support vector machines.
Jianlin Cheng, Arlo Randall, Pierre Baldi. Proteins 2006
Jianlin Cheng, Arlo Randall, Pierre Baldi. Proteins 2006
11
dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction.
Lisa M Kaminskas, Douglas E V Pires, David B Ascher. Sci Rep 2019
Lisa M Kaminskas, Douglas E V Pires, David B Ascher. Sci Rep 2019
33
Understanding molecular consequences of putative drug resistant mutations in Mycobacterium tuberculosis.
Stephanie Portelli, Jody E Phelan, David B Ascher, Taane G Clark, Nicholas Furnham. Sci Rep 2018
Stephanie Portelli, Jody E Phelan, David B Ascher, Taane G Clark, Nicholas Furnham. Sci Rep 2018
20
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
Huali Cao, Jingxue Wang, Liping He, Yifei Qi, John Z Zhang. J Chem Inf Model 2019
11
Prediction of rifampicin resistance beyond the RRDR using structure-based machine learning approaches.
Stephanie Portelli, Yoochan Myung, Nicholas Furnham, Sundeep Chaitanya Vedithi, Douglas E V Pires, David B Ascher. Sci Rep 2020
Stephanie Portelli, Yoochan Myung, Nicholas Furnham, Sundeep Chaitanya Vedithi, Douglas E V Pires, David B Ascher. Sci Rep 2020
57
MAESTROweb: a web server for structure-based protein stability prediction.
Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner. Bioinformatics 2016
Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner. Bioinformatics 2016
11
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
Tiziana Sanavia, Giovanni Birolo, Ludovica Montanucci, Paola Turina, Emidio Capriotti, Piero Fariselli. Comput Struct Biotechnol J 2020
19
MAESTRO--multi agent stability prediction upon point mutations.
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
Josef Laimer, Heidi Hofer, Marko Fritz, Stefan Wegenkittl, Peter Lackner. BMC Bioinformatics 2015
11
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
Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal, Piero Fariselli. BMC Bioinformatics 2019
23
In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity.
Douglas E V Pires, Jing Chen, Tom L Blundell, David B Ascher. Sci Rep 2016
Douglas E V Pires, Jing Chen, Tom L Blundell, David B Ascher. Sci Rep 2016
10
Comparative protein modelling by satisfaction of spatial restraints.
A Sali, T L Blundell. J Mol Biol 1993
A Sali, T L Blundell. J Mol Biol 1993
10
Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource.
Stephanie Portelli, Moshe Olshansky, Carlos H M Rodrigues, Elston N D'Souza, Yoochan Myung, Michael Silk, Azadeh Alavi, Douglas E V Pires, David B Ascher. Nat Genet 2020
Stephanie Portelli, Moshe Olshansky, Carlos H M Rodrigues, Elston N D'Souza, Yoochan Myung, Michael Silk, Azadeh Alavi, Douglas E V Pires, David B Ascher. Nat Genet 2020
21
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
Octav Caldararu, Rukmankesh Mehra, Tom L Blundell, Kasper P Kepp. J Chem Inf Model 2020
35
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
Sirawit Ittisoponpisan, Suhail A Islam, Tarun Khanna, Eman Alhuzimi, Alessia David, Michael J E Sternberg. J Mol Biol 2019
10
Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
10
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
Catherine L Worth, Robert Preissner, Tom L Blundell. Nucleic Acids Res 2011
10
Quantification of biases in predictions of protein stability changes upon mutations.
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
Fabrizio Pucci, Katrien V Bernaerts, Jean Marc Kwasigroch, Marianne Rooman. Bioinformatics 2018
11
PremPS: Predicting the impact of missense mutations on protein stability.
Yuting Chen, Haoyu Lu, Ning Zhang, Zefeng Zhu, Shuqin Wang, Minghui Li. PLoS Comput Biol 2020
Yuting Chen, Haoyu Lu, Ning Zhang, Zefeng Zhu, Shuqin Wang, Minghui Li. PLoS Comput Biol 2020
15
Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
10
SIFT: Predicting amino acid changes that affect protein function.
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
Pauline C Ng, Steven Henikoff. Nucleic Acids Res 2003
8
Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae.
Sundeep Chaitanya Vedithi, Sony Malhotra, Madhusmita Das, Sheela Daniel, Nanda Kishore, Anuja George, Shantha Arumugam, Lakshmi Rajan, Mannam Ebenezer, David B Ascher,[...]. Sci Rep 2018
Sundeep Chaitanya Vedithi, Sony Malhotra, Madhusmita Das, Sheela Daniel, Nanda Kishore, Anuja George, Shantha Arumugam, Lakshmi Rajan, Mannam Ebenezer, David B Ascher,[...]. Sci Rep 2018
18
Structure guided prediction of Pyrazinamide resistance mutations in pncA.
Malancha Karmakar, Carlos H M Rodrigues, Kristy Horan, Justin T Denholm, David B Ascher. Sci Rep 2020
Malancha Karmakar, Carlos H M Rodrigues, Kristy Horan, Justin T Denholm, David B Ascher. Sci Rep 2020
18
Empirical ways to identify novel Bedaquiline resistance mutations in AtpE.
Malancha Karmakar, Carlos H M Rodrigues, Kathryn E Holt, Sarah J Dunstan, Justin Denholm, David B Ascher. PLoS One 2019
Malancha Karmakar, Carlos H M Rodrigues, Kathryn E Holt, Sarah J Dunstan, Justin Denholm, David B Ascher. PLoS One 2019
20
Germline Mutations in the CDKN2B Tumor Suppressor Gene Predispose to Renal Cell Carcinoma.
Mariam Jafri, Naomi C Wake, David B Ascher, Douglas E V Pires, Dean Gentle, Mark R Morris, Eleanor Rattenberry, Michael A Simpson, Richard C Trembath, Astrid Weber,[...]. Cancer Discov 2015
Mariam Jafri, Naomi C Wake, David B Ascher, Douglas E V Pires, Dean Gentle, Mark R Morris, Eleanor Rattenberry, Michael A Simpson, Richard C Trembath, Astrid Weber,[...]. Cancer Discov 2015
8
Bio3d: an R package for the comparative analysis of protein structures.
Barry J Grant, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves. Bioinformatics 2006
Barry J Grant, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves. Bioinformatics 2006
8
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
Ivan A Adzhubei, Steffen Schmidt, Leonid Peshkin, Vasily E Ramensky, Anna Gerasimova, Peer Bork, Alexey S Kondrashov, Shamil R Sunyaev. Nat Methods 2010
8
Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA.
David B Ascher, Jerome Wielens, Tracy L Nero, Larissa Doughty, Craig J Morton, Michael W Parker. Sci Rep 2014
David B Ascher, Jerome Wielens, Tracy L Nero, Larissa Doughty, Craig J Morton, Michael W Parker. Sci Rep 2014
8
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.