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ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations.
Alexey Strokach, Tian Yu Lu, Philip M Kim. J Mol Biol 2021
Times Cited: 6






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



Times Cited
  Times     Co-cited
Similarity


Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
Raphael Guerois, Jens Erik Nielsen, Luis Serrano. J Mol Biol 2002
1174
2
33

iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations.
Cunliang Geng, Anna Vangone, Gert E Folkers, Li C Xue, Alexandre M J J Bonvin. Proteins 2019
24
2
33

MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions.
Ning Zhang, Yuting Chen, Haoyu Lu, Feiyang Zhao, Roberto Vera Alvarez, Alexander Goncearenco, Anna R Panchenko, Minghui Li. iScience 2020
33
2
33

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts.
Peng Xiong, Chengxin Zhang, Wei Zheng, Yang Zhang. J Mol Biol 2017
53
2
33

Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation.
Iain H Moal, Juan Fernandez-Recio. J Chem Theory Comput 2013
23
2
33

A multiscale approach to predicting affinity changes in protein-protein interfaces.
Daniel F A R Dourado, Samuel Coulbourn Flores. Proteins 2014
32
2
33

SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.
Justina Jankauskaite, Brian Jiménez-García, Justas Dapkunas, Juan Fernández-Recio, Iain H Moal. Bioinformatics 2019
85
2
33

BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations.
Yves Dehouck, Jean Marc Kwasigroch, Marianne Rooman, Dimitri Gilis. Nucleic Acids Res 2013
166
2
33

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
105
2
33

PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.
Sherlyn Jemimah, K Yugandhar, M Michael Gromiha. Bioinformatics 2017
30
2
33

A topology-based network tree for the prediction of protein-protein binding affinity changes following mutation.
Menglun Wang, Zixuan Cang, Guo-Wei Wei. Nat Mach Intell 2020
39
2
33

ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification.
Sherlyn Jemimah, Masakazu Sekijima, M Michael Gromiha. Bioinformatics 2020
9
2
33

A simple physical model for binding energy hot spots in protein-protein complexes.
Tanja Kortemme, David Baker. Proc Natl Acad Sci U S A 2002
566
2
33

Mutation effect estimation on protein-protein interactions using deep contextualized representation learning.
Guangyu Zhou, Muhao Chen, Chelsea J T Ju, Zheng Wang, Jyun-Yu Jiang, Wei Wang. NAR Genom Bioinform 2020
14
2
33

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics.
Ehsaneddin Asgari, Mohammad R K Mofrad. PLoS One 2015
200
2
33

Fast and Flexible Protein Design Using Deep Graph Neural Networks.
Alexey Strokach, David Becerra, Carles Corbi-Verge, Albert Perez-Riba, Philip M Kim. Cell Syst 2020
32
2
33

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.
P Gainza, F Sverrisson, F Monti, E Rodolà, D Boscaini, M M Bronstein, B E Correia. Nat Methods 2020
94
2
33

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters.
Wei Su, Meng-Lu Liu, Yu-He Yang, Jia-Shu Wang, Shi-Hao Li, Hao Lv, Fu-Ying Dao, Hui Yang, Hao Lin. J Mol Biol 2021
18
1
16

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive.
Yana Rose, Jose M Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S Rose, Sebastian Bittrich, Stephen K Burley,[...]. J Mol Biol 2021
25
1
16

PolarProtDb: A Database of Transmembrane and Secreted Proteins showing Apical-Basal Polarity.
András Zeke, László Dobson, Levente István Szekeres, Tamás Langó, Gábor E Tusnády. J Mol Biol 2021
3
1
33

aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals.
Federico Zambelli, Matteo Chiara, Erika Ferrandi, Pietro Mandreoli, Marco Antonio Tangaro, Giulio Pavesi, Graziano Pesole. J Mol Biol 2021
1
1
100

MEDUSA: Prediction of Protein Flexibility from Sequence.
Yann Vander Meersche, Gabriel Cretin, Alexandre G de Brevern, Jean-Christophe Gelly, Tatiana Galochkina. J Mol Biol 2021
11
1
16

RiPPMiner-Genome: A Web Resource for Automated Prediction of Crosslinked Chemical Structures of RiPPs by Genome Mining.
Priyesh Agrawal, Sana Amir, Deepak, Drishtee Barua, Debasisa Mohanty. J Mol Biol 2021
6
1
16

BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins.
Giovanni Madeo, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio. J Mol Biol 2021
3
1
33

Cppsite 2.0: An Available Database of Experimentally Validated Cell-Penetrating Peptides Predicting their Secondary and Tertiary Structures.
Kimia Kardani, Azam Bolhassani. J Mol Biol 2021
11
1
16

GCsnap: Interactive Snapshots for the Comparison of Protein-Coding Genomic Contexts.
Joana Pereira. J Mol Biol 2021
1
1
100

ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities.
Jaie Woodard, Chengxin Zhang, Yang Zhang. J Mol Biol 2021
6
1
16

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.
Andrew I Jewett, David Stelter, Jason Lambert, Shyam M Saladi, Otello M Roscioni, Matteo Ricci, Ludovic Autin, Martina Maritan, Saeed M Bashusqeh, Tom Keyes,[...]. J Mol Biol 2021
16
1
16

MPBuilder: A PyMOL Plugin for Building and Refinement of Solubilized Membrane Proteins Against Small Angle X-ray Scattering Data.
D S Molodenskiy, D I Svergun, H D T Mertens. J Mol Biol 2021
4
1
25

interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis.
Maria Filipa Pinto, Antonio Baici, Pedro José Barbosa Pereira, Sandra Macedo-Ribeiro, Annalisa Pastore, Fernando Rocha, Pedro M Martins. J Mol Biol 2021
3
1
33

FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity.
Emma Persson, Miguel Castresana-Aguirre, Davide Buzzao, Dimitri Guala, Erik L L Sonnhammer. J Mol Biol 2021
5
1
20

MPTherm-pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.
A Kulandaisamy, Jan Zaucha, Dmitrij Frishman, M Michael Gromiha. J Mol Biol 2021
5
1
20

ANuPP: A Versatile Tool to Predict Aggregation Nucleating Regions in Peptides and Proteins.
R Prabakaran, Puneet Rawat, Sandeep Kumar, M Michael Gromiha. J Mol Biol 2021
8
1
16

ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases.
Wenliang Zhang, Binghui Zeng, Minglei Yang, Huan Yang, Jianbo Wang, Yongjie Deng, Haiyue Zhang, Guocai Yao, Song Wu, Weizhong Li. J Mol Biol 2021
7
1
16

ModFlex: Towards Function Focused Protein Modeling.
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik. J Mol Biol 2021
2
1
50

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.
Mohamed Kamel, Kristina Kastano, Pablo Mier, Miguel A Andrade-Navarro. J Mol Biol 2021
1
1
100

CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Kohonen Algorithms.
Chakkarai Sathyaseelan, Vinothini Vijayakumar, Thenmalarchelvi Rathinavelan. J Mol Biol 2021
4
1
25

FunRich enables enrichment analysis of OMICs datasets.
Pamali Fonseka, Mohashin Pathan, Sai V Chitti, Taeyoung Kang, Suresh Mathivanan. J Mol Biol 2021
44
1
16

Constrained Standardization of Count Data from Massive Parallel Sequencing.
Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg. J Mol Biol 2021
1
1
100

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.
Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes. J Mol Biol 2021
3
1
33

GeneCaRNA: A Comprehensive Gene-centric Database of Human Non-coding RNAs in the GeneCards Suite.
Ruth Barshir, Simon Fishilevich, Tsippi Iny-Stein, Ofer Zelig, Yaron Mazor, Yaron Guan-Golan, Marilyn Safran, Doron Lancet. J Mol Biol 2021
8
1
16

The DBSAV Database: Predicting Deleteriousness of Single Amino Acid Variations in the Human Proteome.
Jimin Pei, Nick V Grishin. J Mol Biol 2021
6
1
16

geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome.
C Gómez-Martín, E Aparicio-Puerta, J M Medina, Guillermo Barturen, J L Oliver, M Hackenberg. J Mol Biol 2021
1
1
100

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
Robert Fragoza, Jishnu Das, Shayne D Wierbowski, Jin Liang, Tina N Tran, Siqi Liang, Juan F Beltran, Christen A Rivera-Erick, Kaixiong Ye, Ting-Yi Wang,[...]. Nat Commun 2019
23
1
16

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs.
Alessia David, Rozami Razali, Mark N Wass, Michael J E Sternberg. Hum Mutat 2012
102
1
16

Predicting free energy changes using structural ensembles.
Alexander Benedix, Caroline M Becker, Bert L de Groot, Amedeo Caflisch, Rainer A Böckmann. Nat Methods 2009
173
1
16

The Contribution of Missense Mutations in Core and Rim Residues of Protein-Protein Interfaces to Human Disease.
Alessia David, Michael J E Sternberg. J Mol Biol 2015
61
1
16

Spatiotemporal 16p11.2 protein network implicates cortical late mid-fetal brain development and KCTD13-Cul3-RhoA pathway in psychiatric diseases.
Guan Ning Lin, Roser Corominas, Irma Lemmens, Xinping Yang, Jan Tavernier, David E Hill, Marc Vidal, Jonathan Sebat, Lilia M Iakoucheva. Neuron 2015
87
1
16

On human disease-causing amino acid variants: statistical study of sequence and structural patterns.
Marharyta Petukh, Tugba G Kucukkal, Emil Alexov. Hum Mutat 2015
81
1
16

Structural and Computational Characterization of Disease-Related Mutations Involved in Protein-Protein Interfaces.
Dàmaris Navío, Mireia Rosell, Josu Aguirre, Xavier de la Cruz, Juan Fernández-Recio. Int J Mol Sci 2019
8
1
16


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.

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