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Protein interface predictor

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https://www.readbyqxmd.com/read/29753757/dpp-pseaac-a-dna-binding-protein-prediction-model-using-chou-s-general-pseaac
#1
M Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M Kaykobad, M Sohel Rahman
A DNA-binding protein (DNA-BP) is a protein that can bind and interact with a DNA. Identification of DNA-BPs using experimental methods is expensive as well as time consuming. As such, fast and accurate computational methods are sought for predicting whether a protein can bind with a DNA or not. In this paper, we focus on building a new computational model to identify DNA-BPs in an efficient and accurate way. Our model extracts meaningful information directly from the protein sequences, without any dependence on functional domain or structural information...
May 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29662108/nips-a-3d-network-integrated-predictor-of-deleterious-protein-saps-and-its-application-in-cancer-prognosis
#2
Bo Wang, Jing Li, Xi Cheng, Qiao Zhou, Jingxu Yang, Menghuan Zhang, Haifeng Chen, Jing Li
Identifying deleterious mutations remains a challenge in cancer genome sequencing projects, reflecting the vast number of candidate mutations per tumour and the existence of interpatient heterogeneity. Based on a 3D protein interaction network profiled via large-scale cross-linking mass spectrometry, we propose a weighted average formula involving the combination of three types of information into a 'meta-score'. We assume that a single amino acid polymorphism (SAP) may have a deleterious effect if the mutation rarely occurs naturally during evolution, if it inhibits binding between a pair of interacting proteins when located at their interface, or if it plays an important role in a protein interaction (PPI) network...
April 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29443925/pclass-protein-quaternary-structure-classification-by-using-bootstrapping-strategy-as-model-selection
#3
Chi-Chou Huang, Chi-Chang Chang, Chi-Wei Chen, Shao-Yu Ho, Hsung-Pin Chang, Yen-Wei Chu
Protein quaternary structure complex is also known as a multimer, which plays an important role in a cell. The dimer structure of transcription factors is involved in gene regulation, but the trimer structure of virus-infection-associated glycoproteins is related to the human immunodeficiency virus. The classification of the protein quaternary structure complex for the post-genome era of proteomics research will be of great help. Classification systems among protein quaternary structures have not been widely developed...
February 14, 2018: Genes
https://www.readbyqxmd.com/read/29409446/exploring-the-potential-of-3d-zernike-descriptors-and-svm-for-protein-protein-interface-prediction
#4
Sebastian Daberdaku, Carlo Ferrari
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function...
February 6, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29348201/solution-structure-of-sperm-lysin-yields-novel-insights-into-molecular-dynamics-of-rapid-protein-evolution
#5
Damien B Wilburn, Lisa M Tuttle, Rachel E Klevit, Willie J Swanson
Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins that are part of systems under arms race dynamics often evolve at unparalleled rates that can produce atypical biochemical properties. In the marine mollusk abalone, lysin and vitelline envelope receptor for lysin (VERL) are a pair of rapidly coevolving proteins that are essential for species-specific interactions between sperm and egg...
February 6, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29127686/the-challenge-of-modeling-protein-assemblies-the-casp12-capri-experiment
#6
Marc F Lensink, Sameer Velankar, Minkyung Baek, Lim Heo, Chaok Seok, Shoshana J Wodak
We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP-CAPRI protein assembly prediction experiment. These targets comprised 12 homo-oligomers and 3 hetero-complexes. The bulk of the analysis focuses on 10 targets (of CAPRI Round 37), which included all 3 hetero-complexes, and whose protein chains or the full assembly could be readily modeled from structural templates in the PDB. On average, 28 CAPRI groups and 10 CASP groups (including automatic servers), submitted models for each of these 10 targets...
March 2018: Proteins
https://www.readbyqxmd.com/read/29071742/assessment-of-protein-assembly-prediction-in-casp12
#7
Aleix Lafita, Spencer Bliven, Andriy Kryshtafovych, Martino Bertoni, Bohdan Monastyrskyy, Jose M Duarte, Torsten Schwede, Guido Capitani
We present the results of the first independent assessment of protein assemblies in CASP. A total of 1624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. We evaluated the accuracy of oligomeric predictions by comparison to their reference structures at the interface patch and residue contact levels. We find that interface patches are more reliably predicted than the specific residue contacts. Whereas none of the 15 hard oligomeric targets have successful predictions for the residue contacts at the interface, six have models with resemblance in the interface patch...
March 2018: Proteins
https://www.readbyqxmd.com/read/28990628/computational-identification-of-protein-s-sulfenylation-sites-by-incorporating-the-multiple-sequence-features-information
#8
Md Mehedi Hasan, Dianjing Guo, Hiroyuki Kurata
Cysteine S-sulfenylation is a major type of posttranslational modification that contributes to protein structure and function regulation in many cellular processes. Experimental identification of S-sulfenylation sites is challenging, due to the low abundance of proteins and the inefficient experimental methods. Computational identification of S-sulfenylation sites is an alternative strategy to annotate the S-sulfenylated proteome. In this study, a novel computational predictor SulCysSite was developed for accurate prediction of S-sulfenylation sites based on multiple sequence features, including amino acid index properties, binary amino acid codes, position specific scoring matrix, and compositions of profile-based amino acids...
November 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28968673/intpred-a-structure-based-predictor-of-protein-protein-interaction-sites
#9
Tom Northey, Anja Barešic, Andrew C R Martin
Motivation: Protein-protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein-protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein-protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods...
September 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28901589/the-subcons-webserver-a-user-friendly-web-interface-for-state-of-the-art-subcellular-localization-prediction
#10
M Salvatore, N Shu, A Elofsson
SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts...
January 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28867223/protein-protein-interaction-site-predictions-with-minimum-covariance-determinant-and-mahalanobis-distance
#11
Zhijun Qiu, Bo Zhou, Jiangfeng Yuan
Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data errors are often brought into the training dataset. In response to these two problems, we used the minimum covariance determinant (MCD) method to refine the training data to build a predictor with better performance, utilizing its ability of removing outliers. In order to predict test data in practice, a method based on Mahalanobis distance was devised to select proper test data as input for the predictor...
September 1, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28808256/spoton-high-accuracy-identification-of-protein-protein-interface-hot-spots
#12
Irina S Moreira, Panagiotis I Koukos, Rita Melo, Jose G Almeida, Antonio J Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H Gümüş, Joaquim Costa, Alexandre M J J Bonvin
We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with a demonstrated accuracy of 0.95 and sensitivity of 0.98 on an independent test set. The predictor was developed using an ensemble machine learning approach with up-sampling of the minor class. It was trained on 53 complexes using various features, based on both protein 3D structure and sequence. The SpotOn web interface is freely available at: http://milou...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#13
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28575181/deepsite-protein-binding-site-predictor-using-3d-convolutional-neural-networks
#14
J Jiménez, S Doerr, G Martínez-Rosell, A S Rose, G De Fabritiis
Motivation: An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Results: Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples...
October 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28393267/charting-the-perfect-storm-emerging-biological-interfaces-between-stress-and-stroke
#15
REVIEW
G Kronenberg, J Schöner, C Nolte, A Heinz, M Endres, Karen Gertz
A growing body of evidence demonstrates that psychosocial stress is an important and often underestimated risk factor for cardiovascular disease such as myocardial infarction and stroke. In this article, we map out major biological interfaces between stress, stress-related psychiatric disorders, and stroke, placing special emphasis on the fact that stress and psychiatric disorders may be both cause and consequence of cardiovascular disease. Apart from high-risk lifestyle habits such as smoking and lack of exercise, neuroendocrine dysregulation, alterations of the hemostatic system, increased oxidative stress, and inflammatory changes have been implicated in stress-related endothelial dysfunction...
April 9, 2017: European Archives of Psychiatry and Clinical Neuroscience
https://www.readbyqxmd.com/read/28345534/electron-transfer-processes-occurring-on-platinum-neural-stimulating-electrodes-calculated-charge-storage-capacities-are-inaccessible-during-applied-stimulation
#16
Eric M Hudak, Doe W Kumsa, Heidi B Martin, J Thomas Mortimer
OBJECTIVE: Neural prostheses employing platinum electrodes are often constrained by a charge/charge-density parameter known as the Shannon limit. In examining the relationship between charge injection and observed tissue damage, the electrochemistry at the electrode-tissue interface should be considered. The charge-storage capacity (CSC) is often used as a predictor of how much charge an electrode can inject during stimulation, but calculating charge from a steady-state i-E curve (cyclic voltammogram) over the water window misrepresents how electrodes operate during stimulation...
August 2017: Journal of Neural Engineering
https://www.readbyqxmd.com/read/28073761/seeing-the-trees-through-the-forest-sequence-based-homo-and-heteromeric-protein-protein-interaction-sites-prediction-using-random-forest
#17
Qingzhen Hou, Paul F G De Geest, Wim F Vranken, Jaap Heringa, K Anton Feenstra
Motivation: Genome sequencing is producing an ever-increasing amount of associated protein sequences. Few of these sequences have experimentally validated annotations, however, and computational predictions are becoming increasingly successful in producing such annotations. One key challenge remains the prediction of the amino acids in a given protein sequence that are involved in protein-protein interactions. Such predictions are typically based on machine learning methods that take advantage of the properties and sequence positions of amino acids that are known to be involved in interaction...
May 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27792167/predicting-protein-protein-interaction-sites-using-sequence-descriptors-and-site-propensity-of-neighboring-amino-acids
#18
Tzu-Hao Kuo, Kuo-Bin Li
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging task. Using a statistical learning technique, we proposed a computational tool for predicting PPI interaction sites. As an alternative to similar approaches requiring structural information, the proposed method takes all of the input from protein sequences. In addition to typical sequence features, our method takes into consideration that interaction sites are not randomly distributed over the protein sequence...
October 26, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27667482/modeling-oblong-proteins-and-water-mediated-interfaces-with-rosettadock-in-capri-rounds-28-35
#19
Nicholas A Marze, Jeliazko R Jeliazkov, Shourya S Roy Burman, Scott E Boyken, Frank DiMaio, Jeffrey J Gray
The 28th-35th rounds of the Critical Assessment of PRotein Interactions (CAPRI) served as a practical benchmark for our RosettaDock protein-protein docking protocols, highlighting strengths and weaknesses of the approach. We achieved acceptable or better quality models in three out of 11 targets. For the two α-repeat protein-green fluorescent protein (αrep-GFP) complexes, we used a novel ellipsoidal partial-global docking method (Ellipsoidal Dock) to generate models with 2.2 Å/1.5 Å interface RMSD, capturing 49%/42% of the native contacts, for the 7-/5-repeat αrep complexes...
March 2017: Proteins
https://www.readbyqxmd.com/read/27383535/fastrnabindr-fast-and-accurate-prediction-of-protein-rna-interface-residues
#20
Yasser El-Manzalawy, Mostafa Abbas, Qutaibah Malluhi, Vasant Honavar
A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences...
2016: PloS One
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