Search · four archives
Search · four archives
27 papers · ranked by Valyu relevance
Shweta B. Shah, Nikolaos V. Sahinidis, Vasilis J. Promponas
Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights…
Cameron L.M. Gilchrist, Milot Mirdita, Martin Steinegger
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available proteins structures, requiring fast and accurate MSTA methods. Here, we introduce FoldMason, a…
Che-Lun Hung, Yaw-Ling Lin
Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the…
James H. Collier, Lloyd Allison, Arthur M. Lesk, Peter J. Stuckey + 2 more
Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates.) Despite its importance, the structural alignment…
Zhuoyang Chen, Xuechen Zhang, Weichuan Yu, Qiong Luo
In this study, we investigate the performance of nine protein structure alignment tools by analyzing the influence of alignment results in accomplishing three downstream biological tasks: homology detection, phylogeny reconstruction, and function inference. These tools include (1) traditional sequential methods using…
Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma R Chandra
Background Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed…
Olga Ivanova, Jose Gavaldá-García, Dea Gogishvili, Isabel Houtkamp + 3 more
'Robbin Bouwmeester' 'K. Anton Feenstra' 'Sanne Abeln'] | 3 | Structure Alignment | | 1 | | --- | --- | --- | --- | | | Olga Ivanova | Jose Gavald´a-Garc´ıa Dea Gogishvili | | | | Isabel Houtkamp | Robbin Bouwmeester | | | | K. Anton Feenstra | Sanne Abeln | | | | 1 Comparing protein structures | | 4 | | | | 1.1…
Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma R Chandra
Background In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly important research issue. This paper reports an algorithm, motivated from spectral graph matching…
Paul Shealy, Homayoun Valafar
Background Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that…
Gundolf Schenk, Thomas Margraf, Andrew E Torda
Background Protein structure alignments are usually based on very different techniques to sequence alignments. We propose a method which treats sequence, structure and even combined sequence + structure in a single framework. Using a probabilistic approach, we calculate a similarity measure which can be applied to…
Shalini Bhattacharjee, Asish Mukhopadhyay
The alignment of two protein structures is a fundamental problem in structural bioinformatics. In this paper, we propose a novel approach to measure the effectiveness of a sample of three such algorithms, DALI, TM-align and EDAlign_sse_. The underlying premise of our approach is that structural proximity should…
Paul Shealy, Homayoun Valafar
- Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an algorithm (msTALI) for aligning multiple protein structures using biochemical and…
Abel Rodríguez, Scott C. Schmidler
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of…
Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos + 1 more
'Damien P. Devos' 'Francisco Melo'] Background The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method…
Sarika Kondra, Titli Sarkar, Vijay Raghavan, Wu Xu
Development of protein 3-D structural comparison methods is important in understanding protein functions. At the same time, developing such a method is very challenging. In the last 40 years, ever since the development of the first automated structural method, ~200 papers were published using different representations…
Kaushik Roy, Satish Chandra Panigrahi, Asish K. Mukhopadhyay
Protein structure comparison has long been under investigation by computational biologists in hopes for finding a better but not necessarily faster alternative to the more familiar multiple sequence alignment problem. The multiple alignment problem is more challenging than pairwise alignment even for sequences, and we…
Barış Ekim
— Identification and alignment of threedimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of patterns and motifs in mutual structural fragments. With the exponential…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
Rezaul Karim, Mohd. Momin Al Aziz, Swakkhar Shatabda, M. Sohel Rahman
'M. Sohel Rahman'] Abstract—Protein tertiary structure defines its functions, classification and binding sites. Similar structural characteristics between two proteins often lead to the similar characteristics thereof. Determining structural similarity accurately in real time is a crucial research issue. In this paper…
Jianzhu Ma
Proteins are the basic building blocks of life. They form the basis of hormones, which regulate metabolism, structures such as hair, wool, muscle, and antibodies. In the form of enzymes, they are behind all chemical reactions in the body. They also help our body fight infections, turn food into energy, copy DNA and…
Oscar Piette, David Abia, Ugo Bastolla
Evolutionary inferences depend crucially on the quality of multiple sequence alignments (MSA), which is problematic for distantly related proteins. Since protein structure is more conserved than protein sequence, it seems natural to use structure alignments for distant homologs. However, structure alignments may not be…
Authors not listed
Blinatumomab is an FDA-approved bispecific T Cell engager(BiTE) that binds CD3 on T cells and CD19 on B cells, redirecting cytotoxic T cell activity to malignant B cells. Blinatumomab has achieved clinical success in treating B-cell acute lymphoblastic leukemia(B-ALL), however, the structural and functional…
Authors not listed
Proteochemometric models (PCM) are used in computational drug discovery to leverage both protein and ligand representations for bioactivity prediction. While machine learning (ML) and deep learning (DL) have come to dominate PCMs, often serving as scoring functions, rigorous evaluation standards have not always been…
Authors not listed
Pose prediction of ligands to proteins remains a central challenge of structure-based drug design. Although data leakage and generalizability concerns remain, data-driven methods for pose prediction (i.e. based on deep learning and diffusion) now routinely outperform traditional techniques such as molecular docking. In…
Javier Caceres-Delpiano, Roberto Ibañez, Patricio Alegre, Cynthia Sanhueza + 5 more
Protein sequences are highly dimensional and present one of the main problems for the optimization and study of sequence-structure relations. The intrinsic degeneration of protein sequences is hard to follow, but the continued discovery of new protein structures has shown that there is convergence in terms of the…
Nathan M. Lim, Meghan Osato, Gregory L. Warren, David L. Mobley
Part of early stage drug discovery involves determining how molecules may bind to the target protein. Through understanding where and how molecules bind, chemists can begin to build ideas on how to design improvements to increase binding affinities. In this retrospective study, we compare how computational approaches…
Arun Shanker, Divya Bhanu, Anjani Alluri, Samriddhi Gupta
The family of viruses belonging to Coronaviridae mainly consist of virulent pathogens that have a zoonotic property, Severe Acute Respiratory Syndrome (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV) of this family have emerged before and now the SARS-CoV-2 has emerged in China. Characterization of spike…