Article
Multidisciplinary Sciences
Xia Liu, Minghui Wang, Ao Li
Summary: This study introduces a novel deep-learning framework called PhosVarDeep for predicting phospho-variants, which significantly improves prediction performance through two identical subnetworks and a prediction module. The experimental results demonstrate the effectiveness of this method and its favorable comparison with existing conventional machine learning methods.
Editorial Material
Multidisciplinary Sciences
Luke M. M. Evans, Pamela N. Romero N. Villela
Summary: An analysis of rare genetic variants shows their impact on human traits is mediated through similar biological pathways as common variants, enhancing our understanding of their influence on complex traits.
Article
Biochemistry & Molecular Biology
Abdo A. Elfiky, Ibrahim M. Ibrahim
Summary: Recent studies have shown the association between the Zika virus and the host cell membrane receptor GRP78. Utilizing structural bioinformatics and molecular dynamics simulations, the research predicts the binding site of the ZIKV envelope protein with GRP78, shedding light on the viral recognition mechanism.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara
Summary: Protein-protein docking is a useful tool for modeling protein complex structures and understanding their functional mechanisms. Despite the increasing number of known protein structures, there are still cases where the structures of proteins for docking are unknown. This study integrated the AttentiveDist method for protein structure prediction into the LZerD docking webserver, allowing users to submit protein sequences and obtain full-complex atomic models without providing any structure themselves.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemical Research Methods
Tzu-Hsuan Wu, Peng-Chan Lin, Hsin-Hung Chou, Meng-Ru Shen, Sun-Yuan Hsieh
Summary: In this study, machine learning methods and Rosetta Energy Function 2015 were combined to predict the pathogenicity of single amino acid variants (SAVs). The accuracy level of the proposed model (0.76) was higher than that of six other prediction tools. Differential reference energies, attractive energies, and solvation of polar atoms between wildtype and mutant side-chains played essential roles in distinguishing benign from pathogenic variants. These findings suggest that energy scores calculated from protein structures are more appropriate and detailed representations of SAV pathogenicity.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Shangbo Ning, Huiwen Wang, Chen Zeng, Yunjie Zhao
Summary: Cyclin-dependent kinase (Cdk) proteins are important in cell cycle progression and can be targeted for therapy against diseases like cancer. Current Cdk inhibitors lack specificity and often have side effects, making it necessary to identify and study non-catalytic pockets that can interfere with kinase activity. This article summarizes the existing Cdk pockets and their selectivity, introduces a network-based pocket prediction approach called NetPocket, and discusses potential future directions and challenges.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Pietro Bongini, Neri Niccolai, Alfonso Trezza, Guido Mangiavacchi, Annalisa Santucci, Ottavia Spiga, Monica Bianchini, Simone Gardini
Summary: By using a structural bioinformatic approach, the researchers investigated the amino acid compositions at interfaces between small molecules and proteins. They found that glycine (Gly) was highly abundant at enzyme catalytic sites and suggested that it plays a fundamental role in stabilizing concave protein surface moieties. Additionally, they attempted to predict the effect of Gly mutations in a specific protein to create new surface pockets and alter protein activity.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
P. Bryant, G. Pozzati, A. Elofsson
Summary: Predicting the structure of protein complexes is extremely challenging. In this study, the authors utilize AlphaFold2 combined with optimized multiple sequence alignments to model interacting protein complexes, achieving state-of-the-art accuracy in predicting both the interaction status and mode of proteins.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Oussema Khamessi, Hazem Ben Mabrouk, Selim Kamoun, Chaima Hkimi, Kais Ghedira, Riadh Kharrat
Summary: Snake venom contains active molecules called disintegrins which have shown to be highly effective in inhibiting tumor growth. This study investigated the structure of three KTS-disintegrins and their interaction with the alpha 1 beta 1 integrin receptor. The results revealed that the flexibility of the KTSR motif and the C-terminal region play a crucial role in the interaction. These findings provide insights into the structural differences of KTS-disintegrins and their interactions with the alpha 1 beta 1 receptors, which can aid in the development of targeted antitumor therapies.
Article
Biochemistry & Molecular Biology
Deborah Giordano, Cassiano Langini, Amedeo Caflisch, Anna Marabotti, Angelo Facchiano
Summary: The study compares the structures and flexibility of transglutaminase enzymes from Kutzneria albida (KalbTGase) and Streptomyces mobaraensis (MTGase). It is found that KalbTGase is more rigid and has a more closed catalytic site at room temperature, indicating higher selectivity compared to MTGase. Preliminary results at higher temperature suggest enhanced flexibility of KalbTGase, potentially allowing it to adapt to different substrates, while MTGase shows reduced adaptability and catalytic activity at higher temperatures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Swarnendu Tripathi, Nikita R. Dsouza, Angela J. Mathison, Elise Leverence, Raul Urrutia, Michael T. Zimmermann
Summary: This study reports computational scores for interpreting disease-associated genomic variation in the RAS family of genes. By using a combination of experimental datasets and computational methods, the research found a high correlation between 3D structure-based scores and experimental measures, indicating the impact of biochemical scores on the functional behavior of variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas
Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Chandran S. Abhinand, Athira A. Prabhakaran, Anand Krishnamurthy, Rajesh Raju, Thottethodi Subrahmanya Keshava Prasad, Achuthsankar S. Nair, Kallikat N. Rajasekharan, Oommen V. Oommen, Perumana R. Sudhakaran
Summary: The study investigates the correlation between the binding affinity of mutated S-proteins of SARS-CoV-2 variants and their rate of infectivity. A computational model is developed to predict the infectivity rate of SARS-CoV-2 variants. By mutating a peptide, the peptide with the highest binding affinity is identified and its stability is examined. The study suggests a potential peptide inhibitor for blocking the viral entry to human cells.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Xiaoxiao Zhang, Minjie Xu, Zengrui Wu, Guixia Liu, Yun Tang, Weihua Li
Summary: Structure-based prediction of a compound's potential sites of metabolism mediated by cytochromes P450 is advantageous in drug discovery, with CYP2C9 being a major drug-metabolizing enzyme. Evaluation of different factors showed that certain scoring functions performed better, and crystal structure models had varying effects on prediction accuracy.
Editorial Material
Biochemical Research Methods
Ilya A. Vakser
Summary: Structural characterization of protein interactions is crucial for understanding and manipulating physiological processes. Computational modeling of protein complexes using Deep Learning techniques has revolutionized protein structure prediction and interaction prediction. Schweke et al.'s study presents a community-wide investigation into distinguishing physiological protein-protein complexes/interfaces from non-physiological ones, providing a benchmark set and evaluating various scoring functions and AlphaFold predictions.
Article
Biochemistry & Molecular Biology
Cora Blazquez-Bermejo, Lidia Carreno-Gago, David Molina-Granada, Josu Aguirre, Javier Ramon, Javier Torres-Torronteras, Raquel Cabrera-Perez, Miguel Angel Martin, Cristina Dominguez-Gonzalez, Xavier de la Cruz, Anne Lombes, Elena Garcia-Arumi, Ramon Marti, Yolanda Camara
Article
Biochemistry & Molecular Biology
Mireia Rosell, Luis A. Rodriguez-Lumbreras, Miguel Romero-Durana, Brian Jimenez-Garcia, Lucia Diaz, Juan Fernandez-Recio
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Hematology
Laura Vinas-Gimenez, Laura Donadeu, Laia Alsina, Rafael Rincon, Elena alvarez de la Campa, Ana Esteve-Sole, Albert Catala, Roger Colobran, Xavier de la Cruz, Joan Sayos, Monica Martinez-Gallo
INTERNATIONAL JOURNAL OF HEMATOLOGY
(2020)
Article
Immunology
Laura Vinas-Gimenez, Natalia Padilla, Laura Batlle-Maso, Ferran Casals, Jacques G. Riviere, Monica Martinez-Gallo, Xavier de la Cruz, Roger Colobran
FRONTIERS IN IMMUNOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Mireia Rosell, Juan Fernandez-Recio
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2020)
Article
Medical Laboratory Technology
Lidia Feliubadalo, Alejandro Moles-Fernandez, Marta Santamarina-Pena, Alysson T. Sanchez, Anael Lopez-Novo, Luz-Marina Porras, Ana Blanco, Gabriel Capella, Miguel de la Hoya, Ignacio J. Molina, Ana Osorio, Marta Pineda, Daniel Rueda, Xavier de la Cruz, Orland Diez, Clara Ruiz-Ponte, Sara Gutierrez-Enriquez, Ana Vega, Conxi Lazaro
Summary: This study successfully improved and standardized variant classification for the ATM gene through collaborative efforts, resulting in a reduction of variants of uncertain significance. It highlights the importance of data sharing, data curation, and expertise in achieving improved variant classification.
CLINICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Laura Bryant, Dong Li, Samuel G. Cox, Dylan Marchione, Evan F. Joiner, Khadija Wilson, Kevin Janssen, Pearl Lee, Michael E. March, Divya Nair, Elliott Sherr, Brieana Fregeau, Klaas J. Wierenga, Alexandrea Wadley, Grazia M. S. Mancini, Nina Powell-Hamilton, Jiddeke van de Kamp, Theresa Grebe, John Dean, Alison Ross, Heather P. Crawford, Zoe Powis, Megan T. Cho, Marcia C. Willing, Linda Manwaring, Rachel Schot, Caroline Nava, Alexandra Afenjar, Davor Lessel, Matias Wagner, Thomas Klopstock, Juliane Winkelmann, Claudia B. Catarino, Kyle Retterer, Jane L. Schuette, Jeffrey W. Innis, Amy Pizzino, Sabine Luttgen, Jonas Denecke, Tim M. Strom, Kristin G. Monaghan, Zuo-Fei Yuan, Holly Dubbs, Renee Bend, Jennifer A. Lee, Michael J. Lyons, Julia Hoefele, Roman Gunthner, Heiko Reutter, Boris Keren, Kelly Radtke, Omar Sherbini, Cameron Mrokse, Katherine L. Helbig, Sylvie Odent, Benjamin Cogne, Sandra Mercier, Stephane Bezieau, Thomas Besnard, Sebastien Kury, Richard Redon, Karit Reinson, Monica H. Wojcik, Katrin Ounap, Pilvi Ilves, A. Micheil Innes, Kristin D. Kernohan, Gregory Costain, M. Stephen Meyn, David Chitayat, Elaine Zackai, Anna Lehman, Hilary Kitson, Martin G. Martin, Julian A. Martinez-Agosto, Stan F. Nelson, Christina G. S. Palmer, Jeanette C. Papp, Neil H. Parker, Janet S. Sinsheimer, Eric Vilain, Jijun Wan, Amanda J. Yoon, Allison Zheng, Elise Brimble, Giovanni Battista Ferrero, Francesca Clementina Radio, Diana Carli, Sabina Barresi, Alfredo Brusco, Marco Tartaglia, Jennifer Muncy Thomas, Luis Umana, Marjan M. Weiss, Garrett Gotway, K. E. Stuurman, Michelle L. Thompson, Kirsty McWalter, Constance T. R. M. Stumpel, Servi J. C. Stevens, Alexander P. A. Stegmann, Kristian Tveten, Arve Vollo, Trine Prescott, Christina Fagerberg, Lone Walentin Laulund, Martin J. Larsen, Melissa Byler, Robert Roger Lebel, Anna C. Hurst, Joy Dean, Samantha A. Schrier Vergano, Jennifer Norman, Saadet Mercimek-Andrews, Juanita Neira, Margot Van Allen, Nicola Longo, Elizabeth Sellars, Raymond J. Louie, Sara S. Cathey, Elly Brokamp, Delphine Heron, Molly Snyder, Adeline Vanderver, Celeste Simon, Xavier de la Cruz, Natalia Padilla, J. Gage Crump, Wendy Chung, Benjamin Garcia, Hakon H. Hakonarson, Elizabeth J. Bhoj
Article
Developmental Biology
Simona Iacobucci, Natalia Padilla, Martina Gabrielli, Claudia Navarro, Marta Lombardi, Marta Vicioso-Mantis, Claudia Verderio, Xavier de la Cruz, Marian A. Martinez-Balbas
Summary: The study highlights the crucial role of PHF8 in astrocyte development, particularly in regulating gene expression to influence neuronal synapse formation and maturation. These findings provide insights into the involvement of epigenetics in intellectual disability.
Article
Biochemistry & Molecular Biology
Selen Ozkan, Natalia Padilla, Xavier de la Cruz
Summary: The study confirmed the utility of using endophenotype predictions in the pathogenicity prediction of BRCA1/2 variants and suggested different options for future improvements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Marc F. Lensink, Guillaume Brysbaert, Theo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Gieldon, Mateusz Kogut, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Martyna Maszota-Zieleniak, Adam K. Sieradzan, Rafal Slusarz, Patryk A. Wesolowski, Karolina Zieba, Carlos A. Del Carpio Munoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jimenez-Garcia, Panagiotis I. Koukos, Siri Van Keulen, Charlotte W. Van Noort, Manon Reau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A. Rodriguez-Lumbreras, Juan Fernandez-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkunas, Kliment Olechnovic, Ceslovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak
Summary: The results of the CAPRI Round 50 showed that 25 groups participated in submitting models for 12 targets, with a good level of accuracy overall.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Cinthia Aguilera, Elisabeth Gabau, Ariadna Ramirez-Mallafre, Carme Brun-Gasca, Jana Dominguez-Carral, Veronica Delgadillo, Steve Laurie, Sophia Derdak, Natalia Padilla, Xavier de la Cruz, Nuria Capdevila, Nino Spataro, Neus Baena, Miriam Guitart, Anna Ruiz
Summary: Our results show a wide genetic heterogeneity in AS-like patients, with identified variants in multiple neurodevelopmental genes, expanding the differential diagnosis.
Article
Oncology
Mireia Olivan, Marta Garcia, Leticia Suarez, Marc Guiu, Laura Gros, Olga Mendez, Marina Rigau, Jaume Reventos, Miguel F. Segura, Ines de Torres, Jacques Planas, Xavier de la Cruz, Roger R. Gomis, Juan Morote, Ruth Rodriguez-Barrueco, Anna Santamaria
Summary: Around 70% of advanced-stage prostate cancer (PCa) patients will experience bone metastasis, severely affecting patients' quality of life and typically progressing to lethal PCa. Understanding the molecular heterogeneity of PCa cell populations and the signaling pathways associated with bone tropism is crucial. This study provides a genomic signature involved in PCa bone growth, contributing to a better understanding of the mechanisms responsible for this process.
Article
Biochemistry & Molecular Biology
Josu Aguirre, Natalia Padilla, Selen Ozkan, Casandra Riera, Lidia Feliubadalo, Xavier de la Cruz
Summary: Pathogenicity predictors are computational tools used in genomic medicine to classify genetic variants as benign or pathogenic. Selecting the most suitable tool from over 50 available predictors for clinical applications has become increasingly challenging. To address this issue, a cost-based framework that considers clinical scenarios and treats predictors as rejection classifiers was developed. Results showed that no single predictor is optimal for all clinical scenarios and considering rejection provides a different perspective on classifiers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Mireia Rosell, Juan Fernandez-Recio
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)