The computational metabolomics field brings together computer scientists, bioinformaticians, chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide array of scientific and medical disciplines. The field continues to... Read More
Computational Biology Research Articles
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Recent advances in mass spectrometry-based computational metabolomics
- Current Opinion in Chemical Biology
- VOL. 74
on Jun 1, 2023
- Computer Biologists
- Computational Metabolomics
- Interpretation Of Metabolomics Data
- Techniques For Integration Of Data
- Techniques For Visualization
- Medical Disciplines
- More +
Computational characteristics of the structure-activity relationship of inhibitors targeting Pks13-TE domain
- Computational Biology and Chemistry
- VOL. 104
on Jun 1, 2023
- Computational Biology
- Target For Anti-tuberculosis Drug Development
- Hydrogen Bond Donors
- Size Of Binding Pocket
- Computational Biology Techniques
- Size Of Pocket
- More +
Multiple studies have established the Pks13-TE domain as a promising target for anti-tuberculosis drug development. However, recent findings have revealed that the lead compound currently in the pipeline for Pks13-TE has significant cardiotoxicity is... Read More
The confluence of machine learning and multiscale simulations
- Current Opinion in Structural Biology
- VOL. 80
on Jun 1, 2023
- Multiscale Simulation
- Era Of Discovery
- Multiscale Modeling
- Structural Biology
- Deep Learning
- Fine-scale Models
- More +
Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, ha... Read More
Protein structure-based in-silico approaches to drug discovery: Guide to COVID-19 therapeutics
- Molecular Aspects of Medicine
- VOL. 91
on Jun 1, 2023
- Front-line Researchers
- Target-specific Agents
- COVID-19 Therapeutic
- Effective Vaccine Development
- Breakthrough Infections
- Platform For Use
- More +
With more than 5 million fatalities and close to 300 million reported cases, COVID-19 is the first documented pandemic due to a coronavirus that continues to be a major health challenge. Despite being rapid, uncontrollable, and highly infectious in i... Read More
EmPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model
- Briefings in Bioinformatics
on May 16, 2023
- Computational Biology
- Sequential Forward Selection Method
- protein-DNA Binding Affinity
- Ensemble Regression Model
- DNA Structure
- Binding Partners
- More +
Abstract Protein–deoxyribonucleic acid (DNA) interactions are important in a variety of biological processes. Accurately predicting protein-DNA binding affinity has been one of the most attractive and challenging issues in computationa... Read More
Across atoms to crossing continents: Application of similarity measures to biological location data
- PLOS ONE
- VOL. 18
on May 15, 2023
- Computational Biology
- Similarity Measures
- Dynamic Time Warping
- Longest Common Subsequence
- Wasserstein Distance
- Kullback-Leibler Divergence
- More +
Biological processes involve movements across all measurable scales. Similarity measures can be applied to compare and analyze these movements but differ in how differences in movement are aggregated across space and time. The present study reviews f... Read More
LPCAT1 enhances the invasion and migration in gastric cancer: Based on computational biology methods and in vitro experiments
- Cancer Medicine
on May 15, 2023
- Computational Biology
- LPCAT1
- GC
- Migration Of GC
- Protein Expression
- In-house Immunohistochemistry
- More +
The biological functions and clinical implications of lysophosphatidylcholine acyltransferase 1 (LPCAT1) remain unclarified in gastric cancer (GC). The aim of the current study was to explore the possible clinicopathological significance of LPCAT1 an... Read More
Novel computational biology modeling system can accurately forecast response to neoadjuvant therapy in early breast cancer
- Breast Cancer Research
- VOL. 25
on May 10, 2023
- Therapy In Early Breast Cancer
- HR
- Clopper Pearson Interval
- Molecular Characterization Of Tumors
- Residual Tumor Volume
- Triple Negative Breast Cancer
- More +
BackgroundGeneralizable population-based studies are unable to account for individual tumor heterogeneity that contributes to variability in a patient’s response to physician-chosen therapy. Although molecular characterization of tumors has advanced ... Read More
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
- Annual Review of Biophysics
- VOL. 52
on May 9, 2023
- Protein Structure Prediction Field
- Experimental Structural Biology
- Structure Prediction Field
- Modeling Of Complexes
- Blind Experiments
- Deep Learning Methods
- More +
Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have ov... Read More
Local Fractional Strong Metric Dimension of Certain Complex Networks
- Complexity
- VOL. 2023
on May 5, 2023
- Building Blocks Of Complex Networks
- Complex Networks
- Field Of Computer Science
- Dimension Of Networks
- Local Dimension
- Symmetric Networks
- More +
Fractional variants of distance-based parameters have application in the fields of sensor networking, robot navigation, and integer programming problems. Complex networks are exceptional networks which exhibit significant topological features and hav... Read More
Large scale sequence alignment via efficient inference in generative models
- Scientific Reports
- VOL. 13
on May 4, 2023
- Computational Biology
- Large Scale Sequence Alignment
- Independent Probabilities
- Efficient Inference
- Database Size
- Inference Problem
- More +
Finding alignments between millions of reads and genome sequences is crucial in computational biology. Since the standard alignment algorithm has a large computational cost, heuristics have been developed to speed up this task. Though orders of magni... Read More
ROptimus: a parallel general-purpose adaptive optimization engine
- Bioinformatics
- VOL. 39
on May 1, 2023
- Computational Biology
- Optimization Engine
- Desired State
- Configurational Space
- Simulated Replica
- Local Minima
- More +
Summary Motivation Various computational biology calculations require a probabilistic optimization protocol to determine the parameters that capture the system at a desired state in the configuratio... Read More
Verifiable biology
- Journal of The Royal Society Interface
- VOL. 20
on May 1, 2023
- Computational Modelling Approaches
- Biological Systems
- Formal Verification
- Formal Verification Techniques
- Biochemical Networks
- Software Suites
- More +
The formalization of biological systems using computational modelling approaches as an alternative to mathematical-based methods has recently received much interest because computational models provide a deeper mechanistic understanding of biological... Read More
Immunogenic multi-epitope-based vaccine development to combat cyclosporiasis of immunocompromised patients applying computational biology method
- Experimental Parasitology
- VOL. 248
on May 1, 2023
- Illness In Immunocompromised Individuals
- Review Of The Literature
- Cyclospora Cayetanensis Infections
- Digestive Illness
- Vaccine Candidate
- Cyclospora Cayetanensis
- More +
Cyclospora cayetanensis infections, also known as cyclosporiasis, persist to be the prevalent emerging protozoan parasite and an opportunist that causes digestive illness in immunocompromised individuals. In contrast, this causal agent can affect peo... Read More
A comparison between steepest descent and non-linear conjugate gradient algorithms for binding energy minimization of organic molecules
- Journal of Physics: Conference Series
- VOL. 2484
on May 1, 2023
- Steepest Descent Algorithm
- Value Of Binding Free Energy
- Minimum Value Of Energy
- Value Of Free Energy
- Steric Energy
- Conjugate Gradient
- More +
The main intention of optimization is to bring about the “best” of any model by prioritizing the needs along with a given set of constraints. There is a wide range of optimization problems, among which, unfortunately, the problems that are formulated... Read More
Comparative analysis of gene ontology-based semantic similarity measurements for the application of identifying essential proteins
- PLOS ONE
- VOL. 18
on Apr 21, 2023
- Semantic Similarity Metrics
- Annotation Terms
- GO Annotation Terms
- Similarity Metrics
- Original Network
- Semantic Similarity
- More +
Identifying key proteins from protein-protein interaction (PPI) networks is one of the most fundamental and important tasks for computational biologists. However, the protein interactions obtained by high-throughput technology are characterized by a ... Read More
Identification of discriminant features from stationary pattern of nucleotide bases and their application to essential gene classification
- Frontiers in Genetics
- VOL. 14
on Apr 20, 2023
- Essential Genes
- Essential Gene
- Co-occurrence Matrices
- Feature Representation Techniques
- Supervised Machine Learning Algorithms
- Deoxyribonucleic Acid Replication
- More +
Introduction: Essential genes are essential for the survival of various species. These genes are a family linked to critical cellular activities for species survival. These genes are coded for proteins that regulate central metabolism, gene translati... Read More
Potential mechanisms of osthole against bladder cancer cells based on network pharmacology, molecular docking, and experimental validation
- BMC Complementary Medicine and Therapies
- VOL. 23
on Apr 17, 2023
- Bladder Cancer Cells
- STRING
- Bladder Cancer
- Target Gene Fragments
- KEGG
- Co-crystal Ligand
- More +
BackgroundOsthole was traditionally used in treatment for various diseases. However, few studies had demonstrated that osthole could suppress bladder cancer cells and its mechanism was unclear. Therefore, we performed a research to explore the potent... Read More
On the Complexity of String Matching for Graphs
- ACM Transactions on Algorithms
- VOL. 19
on Apr 12, 2023
- Algorithm For Exact String Matching
- SETH
- Node Labels
- Linear Time Solutions
- Regular Expression Matching
- Maximum Node Degree
- More +
Exact string matching in labeled graphs is the problem of searching paths of a graph G=(V, E) such that the concatenation of their node labels is equal to a given pattern string P [1. ... Read More
MiRNA, siRNA, and lncRNAs: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases
- Current Bioinformatics
- VOL. 18
on Apr 11, 2023
- Computational Biologists
- Bioinformatics Tools
- Fields Of Biological Science
- Types Of ncRNA
- Bioinformatics Databases
- Functional RNA Molecule
- More +
Abstract: Today, the bioinformatics tool and database development are one of the most significant research areas in computational biology. Computational biologists are developing diverse bioinformatics tools and databases in the various fields of bi... Read More