Section edited by Lukasz Kurgan
This section incorporates all aspects of structural analysis including but not limited to: methods and applications for the analysis of biological structures, protein structural and biophysical analysis, and structure-based drug design.
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Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a n...
Citation: BMC Bioinformatics 2018 19:146
Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which...
Citation: BMC Bioinformatics 2018 19:138
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 ...
Citation: BMC Bioinformatics 2018 19:35
Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi...
Citation: BMC Bioinformatics 2018 19:29
Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve the...
Citation: BMC Bioinformatics 2018 19:27
Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, e...
Citation: BMC Bioinformatics 2018 19:22
Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial d...
Citation: BMC Bioinformatics 2018 19:18
Hot spots are interface residues that contribute most binding affinity to protein-protein interaction. A compact and relevant feature subset is important for building machine learning methods to predict hot sp...
Citation: BMC Bioinformatics 2018 19:14
RNA structure prediction is an important field in bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict. A...
Citation: BMC Bioinformatics 2018 19:13
RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunate...
Citation: BMC Bioinformatics 2018 19:12
Development of predictors of propensity of protein sequences for successful crystallization has been actively pursued for over a decade. A few novel methods that expanded the scope of these predictions to addr...
Citation: BMC Bioinformatics 2018 18:580
Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being ac...
Citation: BMC Bioinformatics 2017 18:585
Knowledge of catalytic residues can play an essential role in elucidating mechanistic details of an enzyme. However, experimental identification of catalytic residues is a tedious and time-consuming task, whic...
Citation: BMC Bioinformatics 2017 18:583
As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model ...
Citation: BMC Bioinformatics 2017 18:542
Amino acid substitutions due to DNA nucleotide replacements are frequently disease-causing because of affecting functionally important sites. If the substituting amino acid does not fit into the protein, it ca...
Citation: BMC Bioinformatics 2017 18:531
Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein’s function. Numerous standard techniques such as principal component analysis ...
Citation: BMC Bioinformatics 2017 18:525
Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding...
Citation: BMC Bioinformatics 2017 18:493
Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly en...
Citation: BMC Bioinformatics 2017 18:475
Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of ...
Citation: BMC Bioinformatics 2017 18:468
In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the bas...
Citation: BMC Bioinformatics 2017 18:456
Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012,...
Citation: BMC Bioinformatics 2017 18:417
In structural biology area, protein residue-residue contacts play a crucial role in protein structure prediction. Some researchers have found that the predicted residue-residue contacts could effectively const...
Citation: BMC Bioinformatics 2017 18:390
Residue-residue contacts are key features for accurate de novo protein structure prediction. For the optimal utilization of these predicted contacts in folding proteins accurately, it is important to study the...
Citation: BMC Bioinformatics 2017 18:380
In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling t...
Citation: BMC Bioinformatics 2017 18:343
In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein–small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (M...
Citation: BMC Bioinformatics 2017 18:327
Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify...
Citation: BMC Bioinformatics 2017 18:303
Central to protein biology is the understanding of how structural elements give rise to observed function. The surfeit of protein structural data enables development of computational methods to systematically ...
Citation: BMC Bioinformatics 2017 18:302
Bioluminescent proteins (BLPs) widely exist in many living organisms. As BLPs are featured by the capability of emitting lights, they can be served as biomarkers and easily detected in biomedical research, suc...
Citation: BMC Bioinformatics 2017 18:294
RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maxi...
Citation: BMC Bioinformatics 2017 18:290
Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic ste...
Citation: BMC Bioinformatics 2017 18:284
Protein structure prediction has achieved a lot of progress during the last few decades and a greater number of models for a certain sequence can be predicted. Consequently, assessing the qualities of predicte...
Citation: BMC Bioinformatics 2017 18:275
Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two...
Citation: BMC Bioinformatics 2017 18:271
Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide inte...
Citation: BMC Bioinformatics 2017 18:257
Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...
Citation: BMC Bioinformatics 2017 18:220
RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs....
Citation: BMC Bioinformatics 2017 18:136
Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane prote...
Citation: BMC Bioinformatics 2017 18:115
Dystrophinopathy is one of the most common human monogenic diseases which results in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Mutations in the dystrophin gene are responsible for ...
Citation: BMC Bioinformatics 2017 18:87
Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the t...
Citation: BMC Bioinformatics 2017 18:86
RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of...
Citation: BMC Bioinformatics 2017 18:51
Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recogni...
Citation: BMC Bioinformatics 2017 18:27
The cyclin-dependent kinase 2 (CDK2) together with its cyclin E and A partners is a central regulator of cell growth and division. Deregulation of CDK2 activity is associated with diseases such as cancer. The ...
Citation: BMC Bioinformatics 2017 18:15
Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of ...
Citation: BMC Bioinformatics 2016 17:546
Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality...
Citation: BMC Bioinformatics 2016 17:495
Disulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stabili...
Citation: BMC Bioinformatics 2016 17:481
Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function dete...
Citation: BMC Bioinformatics 2016 17:458
Predict whether a mutation is deleterious based on the custom 3D model of a protein.
Citation: BMC Bioinformatics 2016 17:425
RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical...
Citation: BMC Bioinformatics 2016 17:424
Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures...
Citation: BMC Bioinformatics 2016 17:383
According to structure-dependent function of proteins, two main challenging problems called Protein Structure Prediction (PSP) and Inverse Protein Folding (IPF) are investigated. In spite of IPF essential appl...
Citation: BMC Bioinformatics 2016 17:353
Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, and also for discriminating between uni...
Citation: BMC Bioinformatics 2016 17:328
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