A citation-based method for searching scientific literature

Harry C Jubb, Alicia P Higueruelo, Bernardo Ochoa-Montaño, Will R Pitt, David B Ascher, Tom L Blundell. J Mol Biol 2017
Times Cited: 193







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



Times Cited
  Times     Co-cited
Similarity


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
22

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
22

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
21



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
14

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
124
13


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
11

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
9

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2016
76
11

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
39
23

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
65
13

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
9

PLIP: fully automated protein-ligand interaction profiler.
Sebastian Salentin, Sven Schreiber, V Joachim Haupt, Melissa F Adasme, Michael Schroeder. Nucleic Acids Res 2015
782
8

Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy.
Martina Nemethova, Jan Radvanszky, Ludevit Kadasi, David B Ascher, Douglas E V Pires, Tom L Blundell, Berardino Porfirio, Alessandro Mannoni, Annalisa Santucci, Lia Milucci,[...]. Eur J Hum Genet 2016
65
12

mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions.
Douglas E V Pires, David B Ascher. Nucleic Acids Res 2017
68
11

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
29
27

Analysis of a Novel pncA Mutation for Susceptibility to Pyrazinamide Therapy.
Malancha Karmakar, Maria Globan, Janet A M Fyfe, Timothy P Stinear, Paul D R Johnson, Natasha E Holmes, Justin T Denholm, David B Ascher. Am J Respir Crit Care Med 2018
29
27


mmCSM-AB: guiding rational antibody engineering through multiple point mutations.
Yoochan Myung, Douglas E V Pires, David B Ascher. Nucleic Acids Res 2020
21
38

KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks.
José Jiménez, Miha Škalič, Gerard Martínez-Rosell, Gianni De Fabritiis. J Chem Inf Model 2018
296
8

PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting.
Muhammad Radifar, Nunung Yuniarti, Enade Perdana Istyastono. Bioinformation 2013
27
25

BINANA: a novel algorithm for ligand-binding characterization.
Jacob D Durrant, J Andrew McCammon. J Mol Graph Model 2011
124
7

Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.
David B Ascher, Ottavia Spiga, Martina Sekelska, Douglas E V Pires, Andrea Bernini, Monica Tiezzi, Jana Kralovicova, Ivana Borovska, Andrea Soltysova, Birgitta Olsson,[...]. Eur J Hum Genet 2019
36
19

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
29
24

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
23
30

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
32
21

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
7

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
7

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
7

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


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
7


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
32
18


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
71
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
83
7

Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.
Jody Phelan, Francesc Coll, Ruth McNerney, David B Ascher, Douglas E V Pires, Nick Furnham, Nele Coeck, Grant A Hill-Cawthorne, Mridul B Nair, Kim Mallard,[...]. BMC Med 2016
77
7


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
30
20

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
6

Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
6

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
6

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
6

Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.
Maciej Wójcikowski, Michał Kukiełka, Marta M Stepniewska-Dziubinska, Pawel Siedlecki. Bioinformatics 2019
53
11



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
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.