The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first in... Read More
Computational Molecular Biology Research Articles
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LambdaPP : Fast and accessible protein‐specific phenotype predictions
- Protein Science
- VOL. 32
on Dec 19, 2022
- Computational Molecular Biology
- Docker Image
- Protein Sequence
- Intrinsic Disorder
- Python Package
- Phenotype Predictions
- More +
The evolution of structural genomics
- Biophysical Reviews
- VOL. 14
on Dec 15, 2022
- Computational Molecular Biology
- PDBj
- Advances In Deep Learning
- Global Effort
- Unknown Functions
- Large-scale Sequencing Projects
- More +
Structural genomics began as a global effort in the 1990s to determine the tertiary structures of all protein families as a response to large-scale genome sequencing projects. The immediate outcome was an influx of tens of thousands of protein struct... Read More
Markov field models: Scaling molecular kinetics approaches to large molecular machines
- Current Opinion in Structural Biology
- VOL. 77
on Dec 1, 2022
- Markov Field Models
- Molecular Kinetics
- Molecular Dynamics Methods
- Biomolecular Complexes
- Potts Models
- Umbrella Term
- More +
With recent advances in structural biology, including experimental techniques and deep learning-enabled high-precision structure predictions, molecular dynamics methods that scale up to large biomolecular systems are required. Current state-of-the-ar... Read More
BOA: A partitioned view of genome assembly
- iScience
- VOL. 25
on Nov 1, 2022
- Computational Molecular Biology
- Assembly Quality
- Target Genome
- Partial Ordering
- Genome Assembly
- Fundamental Problem
- More +
De novo genome assembly is a fundamental problem in computational molecular biology that aims to reconstruct an unknown genome sequence from a set of short DNA sequences (or reads) obtained from the genome. The relative ordering of the reads along th... Read More
Exact probability of fixed patterns occurring in a random sequence
- Communications in Statistics - Simulation and Computation
- VOL. 51
on Sep 27, 2022
- Computational Molecular Biology
- Random Sequence
- Genetic Sequence Analysis
- Exact Probability
- Single Pattern
- Clinical Medicine
- More +
We derive a procedure to obtain the exact probability that a specific pattern of letters occurs in a longer random sequence of letters. The procedure is generalized to find the exact probability of a fixed (specific) single pattern, and a union or i... Read More
Michael Waterman's Contributions to Computational Biology and Bioinformatics
- Journal of Computational Biology
- VOL. 29
on Jul 1, 2022
- Computational Molecular Biology
- Computational Biology
- RECOMB
- Computational Bioinformatics
- Alignment-free Sequence Comparison
- Computational Genome Analysis
- More +
On the occasion of Dr. Michael Waterman's 80th birthday, we review his major contributions to the field of computational biology and bioinformatics including the famous Smith-Waterman algorithm for sequence alignment, the probability and statistics t... Read More
Protein Structure Prediction Using Quantile Dragonfly and Structural Class-Based Deep Learning
- International Journal of Pattern Recognition and Artificial Intelligence
- VOL. 36
on Mar 14, 2022
- Protein Structure Prediction
- Protein Structure Identification
- Computational Prediction Of Protein Structure
- Protein Structure
- Minimum Execution Time
- Structural Class
- More +
Predicting three-dimensional structure of a protein in the field of computational molecular biology has received greater attention. Most of the recent research works aimed at exploring search space, however with the increasing nature and size of dat... Read More
Identification of alternative protein targets of glutamate-ureido-lysine associated with PSMA tracer uptake in prostate cancer cells
- Proceedings of the National Academy of Sciences
- VOL. 119
on Jan 21, 2022
- Computational Molecular Biology
- Candidate Protein Targets
- Synthetic Chemistry Approach
- PSMA
- Prostate Cancer
- Rapid Identification Of Proteins
- More +
Significance Glutamate-ureido-lysine (GUL) probes are specific for prostate-specific membrane antigen (PSMA), overexpressed by most prostate cancers. This antigen can be lost as the cancer progresses. Recent reports have indicated that GUL ... Read More
An Intelligent Optimization Model for Fragment Assembly Problem
- Fusion: Practice and Applications
on Jan 1, 2022
- Computational Molecular Biology
- HHO
- DNA
- FAP
- Sequence Of DNA
- ABC
- More +
problem as it requires rebuilding the original sequence of DNA from a massive number of fragments. This paper introduces an efficient hybridization between Harris Hawks Optimization (HHO) and Problem Aware Local Search (PALS) to be utilized in solvin... Read More
Computational Methods for Structure-Based Drug Design Through System Biology.
- Methods in molecular biology (Clifton, N.J.)
- VOL. 2385
on Jan 1, 2022
- Computer Molecular Biology
- Virtual Screening Hits
- VS
- Computer Structural Biology
- High-throughput Screening Hits
- Strongest Binding
- More +
The advances in computational chemistry and biology, computer science, structural biology, and molecular biology go in parallel with the rapid progress in target-based systems. This technique has become a powerful tool in medicinal chemistry for the ... Read More
369. Alternative Workflow for SARS-CoV-2 Testing Using a Heat Lysis Protocol for Respiratory Specimens
- Open Forum Infectious Diseases
- VOL. 8
on Nov 1, 2021
- Computational Molecular Biology
- Direct Extraction Protocol
- PCR Platforms
- PCR
- Hologic Panther Fusion
- LoD
- More +
Abstract Background The SARS-CoV-2 pandemic has demonstrated the need for streamlined workflows in high-throughput testing. In extraction-based testing, limited extraction reagents and required prop... Read More
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming.
- Algorithms for molecular biology : AMB
- VOL. 16
on Aug 14, 2021
- MILP
- Graph Search Algorithm
- Chemical Graphs
- MILP Formulation
- ANN
- Two-phase Framework
- More +
Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quantitative structure activity/property relati... Read More
A novel method for inference of acyclic chemical compounds with bounded branch-height based on artificial neural networks and integer programming
- Algorithms for Molecular Biology
- VOL. 16
on Aug 14, 2021
- Graph Search Algorithm
- Chemical Graphs
- MILP
- MILP Formulation
- Two-phase Framework
- Cycle Index
- More +
Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quantitative structure activity/property relat... Read More
Closure properties of bonded sequential insertion-deletion systems
- Journal of Physics: Conference Series
- VOL. 1988
on Jul 1, 2021
- Computer Molecular Biology
- Insertion-deletion System
- Insertion-deletion Systems
- Sequential Systems
- Operations Of Insertion
- Theoretical Computer Science
- More +
Through the years, formal language theory has evolved through continual interdisciplinary work in theoretical computer science, discrete mathematics and molecular biology. The combination of these areas resulted in the birth of DNA computing. Here, l... Read More
Biopython: Comparing the DNA Polymerase I (polA) Gene of Thermophilic, Mesophilic, and Psychrophilic Bacteria
- BiosciED: Journal of Biological Science and Education
- VOL. 2
on Jun 21, 2021
- Computational Molecular Biology
- Psychrophilic Bacteria
- Multiple Sequence Analysis
- polA Gene
- Mesophilic Bacteria
- Thermophilic Bacteria
- More +
Biopython is a specialized Python tool for computational molecular biology. Various computational molecular analysis that can be performed using Biopython, such as reconstructing phylogenetic trees, multiple sequence analysis, generating complementar... Read More
Random Fields in Physics, Biology and Data Science
- Frontiers in Physics
- VOL. 9
on Apr 15, 2021
- Computational Molecular Biology
- Markov Random Fields
- Statistical Physics
- Random Fields
- Fields In Physics
- Data Science
- More +
A random field is the representation of the joint probability distribution for a set of random variables. Markov fields, in particular, have a long standing tradition as the theoretical foundation of many applications in statistical physics and proba... Read More
Metode kompjuterski potpomognutog dizajniranja lekova u istraživanju novih potencijalnih terapeutika za neuropsihijatrijske i inflamatorne bolesti
- Arhiv za farmaciju
- VOL. 71
on Jan 1, 2021
- Computer Molecular Biology
- CADD
- CADD Approaches
- Advances In Computer Sciences
- Serotonin 5-HT2A Receptors
- Rational Drug Design
- More +
Drug discovery and development is a very challenging, expensive and time-consuming process. Impressive technological advances in computer sciences and molecular biology have made it possible to use computer-aided drug design (CADD) methods in various... Read More
Computer Molecular Biology Technology in the Field of Clinical Microbiological Examination
- 2021 International Conference on Applications and Techniques in Cyber Intelligence
on Jan 1, 2021
- Computer Molecular Biology
- Clinical Examination
- Molecular Biology Technology
- Biology Technology
- Microbiological Examination
- Molecular Biology
- More +
The prospects of quantum computing in computational molecular biology
- arXiv: Quantum Physics
on May 26, 2020
- Computational Molecular Biology
- Run Machine Learning Algorithms
- Quantum Computing
- Computational Biology
- Computational Bioinformatics
- Classical Counterparts
- More +
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific disciplines... Read More
The prospects of quantum computing in computational molecular biology
- WIREs Computational Molecular Science
- VOL. 11
on May 22, 2020
- Computational Molecular Biology
- Computational Biology
- Quantum Computing
- Molecular Biology