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<!DOCTYPE html>
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<title>Resources and Tools - Md. Mustak Khan</title>
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<section class="resources-tools-section">
<h1 class="section-title">Resources and Tools</h1>
<div class="resource-category">
<h2 class="category-title">Literature Review Tools</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://unriddle.ai" target="_blank">Unriddle.AI:</a></strong> An AI tool for literature reviews that simplifies reading, extracts key insights, enhances writing, and guides you through complex topics with ease.</li>
<li class="resource-item"><strong><a href="https://www.scienceopen.com" target="_blank">ScienceOpen:</a></strong> A free search engine for research papers with citation metrics, altmetrics, and a user-friendly design for exploring scholarly works.</li>
<li class="resource-item"><strong><a href="https://www.semanticscholar.org" target="_blank">Semantic Scholar:</a></strong> An AI-powered platform for discovering and analyzing academic papers, offering deep insights into scholarly literature.</li>
<li class="resource-item"><strong><a href="https://www.scispace.com" target="_blank">SciSpace:</a></strong> A research tool with 270+ million papers and an AI assistant, Copilot, providing summaries, explanations, and answers to aid comprehension.</li>
<li class="resource-item"><strong><a href="https://picoportal.org" target="_blank">PICO Portal:</a></strong> An AI tool designed to streamline systematic reviews by predicting the most relevant articles based on your criteria.</li>
<li class="resource-item"><strong><a href="https://elicit.org" target="_blank">Elicit:</a></strong> An AI research assistant that helps in literature review by finding relevant papers, summarizing findings, and extracting key information.</li>
<li class="resource-item"><strong><a href="https://www.researchrabbit.com" target="_blank">Research Rabbit:</a></strong> A tool that allows researchers to create collections of papers and visualize the connections between them.</li>
<li class="resource-item"><strong><a href="https://consensus.app" target="_blank">Consensus:</a></strong> An AI-powered search engine that finds and summarizes research papers, helping users quickly understand the consensus in scientific literature.</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Free Courses and Tutorials for Research Methods</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/research-methods" target="_blank">Understanding Research Methods:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.adamacademy.com/courses/write-and-publish-a-research-paper" target="_blank">Write and Publish a Research Paper:</a></strong> By Adam Academy</li>
<li class="resource-item"><strong><a href="https://www.elsevier.com/en-xm/solutions/research-academy" target="_blank">Fundamentals of Manuscript Preparation:</a></strong> By Elsevier Research Academy</li>
<li class="resource-item"><strong><a href="https://www.elsevier.com/en-xm/solutions/research-academy" target="_blank">Writing skills:</a></strong> By Elsevier Research Academy</li>
<li class="resource-item"><strong><a href="https://www.elsevier.com/en-xm/solutions/research-academy" target="_blank">Fundamentals of Publishing:</a></strong> By Elsevier Research Academy</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Find Journals</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://jane.bio" target="_blank">JANE:</a></strong> A tool that helps you find the most relevant journals for your research based on article titles or abstracts.</li>
<li class="resource-item"><strong><a href="https://mjl.clarivate.com" target="_blank">Clarivate Master Journal List:</a></strong> A comprehensive list of journals indexed by Clarivate.</li>
<li class="resource-item"><strong><a href="https://www.scopus.com/sources" target="_blank">Scopus Journal Comparison:</a></strong> Allows you to compare journals indexed in Scopus based on various metrics.</li>
<li class="resource-item"><strong><a href="https://jotjournal.com" target="_blank">Jot:</a></strong> A tool to help you identify the best journals for submitting your manuscript based on keywords or topics.</li>
<li class="resource-item"><strong><a href="https://www.elsevier.com/en-xm/solutions/journal-finder" target="_blank">Elsevier Journal Finder:</a></strong> Helps you find Elsevier journals that match your research topics.</li>
<li class="resource-item"><strong><a href="https://www.taylorandfrancis.com/journal-suggester" target="_blank">Taylor & Francis Journal Suggester:</a></strong> Suggests journals from Taylor & Francis based on the title and abstract of your manuscript.</li>
<li class="resource-item"><strong><a href="https://thinkchecksubmit.org" target="_blank">Think. Check. Submit:</a></strong> A resource to help you evaluate the trustworthiness of journals.</li>
<li class="resource-item"><strong><a href="https://www.wiley.com/en-us/wiley-journal-finder" target="_blank">Wiley Journal Finder:</a></strong> A tool that helps you find Wiley journals by matching your manuscript with relevant journals.</li>
<li class="resource-item"><strong><a href="https://www.cabells.com" target="_blank">Cabell's:</a></strong> Provides a directory of journals and their evaluation metrics.</li>
<li class="resource-item"><strong><a href="https://www.journal-evaluation-tool.com" target="_blank">Journal Evaluation Tool:</a></strong> A tool for evaluating journals based on multiple performance metrics.</li>
<li class="resource-item"><strong><a href="https://sagepub.com/en-us/nam/sage-journal-recommender" target="_blank">Sage Journal Recommender:</a></strong> Suggests Sage journals that are a good fit for your research topic.</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">R Package for Data Analysis</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://dplyr.tidyverse.org" target="_blank">dplyr:</a></strong> A package for data manipulation, offering functions like filtering, selecting, and summarizing data.</li>
<li class="resource-item"><strong><a href="https://tidyr.tidyverse.org" target="_blank">tidyr:</a></strong> Focuses on tidying data, such as reshaping and separating columns.</li>
<li class="resource-item"><strong><a href="https://www.tidyverse.org" target="_blank">Tidyverse:</a></strong> A collection of R packages for consistent data analysis and visualization.</li>
<li class="resource-item"><strong><a href="https://www.danieldsnyder.com/gtsummary" target="_blank">gtsummary & gt:</a></strong> Used for creating customizable summary tables.</li>
<li class="resource-item"><strong><a href="https://ggplot2.tidyverse.org" target="_blank">ggplot2:</a></strong> A powerful visualization package implementing the "grammar of graphics".</li>
<li class="resource-item"><strong><a href="https://hrbrmstr.github.io/hrbrthemes" target="_blank">hrbrthemes:</a></strong> Enhances ggplot2 plots with additional themes.</li>
<li class="resource-item"><strong><a href="https://colorbrewer2.org" target="_blank">RColorBrewer & viridis:</a></strong> Provide color palettes for data visualization.</li>
<li class="resource-item"><strong><a href="https://cran.r-project.org/web/packages/heatmaply/index.html" target="_blank">Heatmaply:</a></strong> Creates interactive heatmaps.</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Free Courses and Tutorials for R Programming</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/data-analysis-with-r" target="_blank">Data Analysis with R Programming:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/r-programming" target="_blank">Introduction to R Programming for Data Science:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/specializations/data-visualization" target="_blank">Data Visualization & Dashboarding with R Specialization:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/specializations/data-science" target="_blank">Expressway to Data Science: R Programming and Tidyverse Specialization:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/specializations/statistical-analysis-r" target="_blank">Statistical Analysis with R for Public Health Specialization:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://chiralscience.com" target="_blank">Mastering R for Research:</a></strong> By CHIRAL Bangladesh [In Bengali Language]</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Data Science Tools</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://numpy.org/" target="_blank">NumPy:</a></strong> Foundation for scientific computing, offering support for multidimensional arrays and mathematical operations.</li>
<li class="resource-item"><strong><a href="https://pandas.pydata.org/" target="_blank">Pandas:</a></strong> Simplifies data wrangling and analysis, providing powerful tools for handling structured data.</li>
<li class="resource-item"><strong><a href="https://matplotlib.org/" target="_blank">Matplotlib:</a></strong> Used for creating static, basic data visualizations.</li>
<li class="resource-item"><strong><a href="https://seaborn.pydata.org/" target="_blank">Seaborn:</a></strong> Enhances Matplotlib with advanced statistical visualizations and attractive aesthetics.</li>
<li class="resource-item"><strong><a href="https://plotly.com/" target="_blank">Plotly:</a></strong> Enables interactive and dynamic data visualizations.</li>
<li class="resource-item"><strong><a href="https://github.com/researchpy/researchpy" target="_blank">researchpy:</a></strong> Data and performs statistical tests efficiently.</li>
<li class="resource-item"><strong><a href="https://dask.org/" target="_blank">Dask:</a></strong> Handles big data analysis with parallel computing support.</li>
<li class="resource-item"><strong><a href="https://scikit-learn.org/" target="_blank">scikit-learn:</a></strong> A versatile library for machine learning, offering tools for classification, regression, and clustering.</li>
<li class="resource-item"><strong><a href="https://scikit-image.org/" target="_blank">scikit-image:</a></strong> Provides tools for image manipulation, especially useful in life sciences.</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Free Courses and Tutorials for Data Science</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/data-analysis-with-python" target="_blank">Data Analysis with Python:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/python-for-applied-data-science-ai" target="_blank">Python for Data Science, AI & Development:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/learn/introduction-to-ai" target="_blank">Introduction to Artificial Intelligence (AI):</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/specializations/machine-learning-introduction" target="_blank">Machine Learning Specialization:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://www.coursera.org/specializations/ai-healthcare" target="_blank">AI in Healthcare Specialization:</a></strong> By Coursera</li>
<li class="resource-item"><strong><a href="https://chiralscience.com" target="_blank">Machine Learning for Bioinformatics:</a></strong> By CHIRAL Bangladesh [In Bengali Language]</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Biological Illustration Tools</h2>
<ul class="resource-list">
<li class="resource-item"><strong><a href="https://www.niaid.nih.gov/research/bioart" target="_blank">BioArt:</a></strong> Hosted by the National Institute of Allergy and Infectious Diseases (NIAID), BioArt provides over 2,000 science and medical visuals, including vectors, icons, and brushes, created by professional illustrators.</li>
<li class="resource-item"><strong><a href="https://bioicons.com/" target="_blank">Bioicon:</a></strong> Bioicon offers a collection of high-quality biological icons and illustrations to enhance scientific presentations and educational materials.</li>
<li class="resource-item"><strong><a href="https://biorender.com/" target="_blank">BioRender:</a></strong> BioRender's scientific illustration software includes an activity sheet with editable lab icons, enabling users to create publication-quality figures using pre-made icons and templates.</li>
<li class="resource-item"><strong><a href="https://scidraw.io/" target="_blank">SciDraw:</a></strong> SciDraw is a platform that offers a variety of scientific drawings, including vectors of cells, animals, and laboratory equipment, contributed by the scientific community.</li>
<li class="resource-item"><strong><a href="https://smart.servier.com/" target="_blank">Servier Medical Art (SMART):</a></strong> It offers over 3,000 free, high-quality medical illustrations suitable for publications and presentations. The collection encompasses various medical specialties, including anatomy, cellular biology, and general medical items.</li>
<li class="resource-item"><strong><a href="https://reactome.org/" target="_blank">Reactome:</a></strong> Reactome is a free, open-source, curated, and peer-reviewed pathway database that provides insights into molecular processes and pathways in human biology.</li>
<li class="resource-item"><strong><a href="https://labicons.net/" target="_blank">LabIcons:</a></strong> LabIcons offers free drawings of laboratory objects to improve knowledge communication in science and education, including clip arts of microcentrifuge tubes, plasticware, instruments, equipment, and glassware.</li>
</ul>
</div>
<div class="resource-category">
<h2 class="category-title">Bioinformatics Tools, Software, and Datasets</h2>
<ul class="resource-list">
<li class="resource-item"><strong>Sequence Retrieval and Analysis:</strong></li>
<li class="resource-item"><strong><a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI Database:</a></strong> Provides access to genomic and protein sequence data for various organisms.</li>
<li class="resource-item"><strong><a href="http://emboss.sourceforge.net/apps/release/6.6/emboss_stretcher.html" target="_blank">EMBOSS Stretcher:</a></strong> Aligns nucleotide or protein sequences using dynamic programming.</li>
<li class="resource-item"><strong><a href="http://prosite.expasy.org/" target="_blank">PROSITE:</a></strong> Identifies protein motifs and conserved functional domains.</li>
<li class="resource-item"><strong>Homology Modeling:</strong></li>
<li class="resource-item"><strong><a href="https://salilab.org/modeller/" target="_blank">Modeller v9.26:</a></strong> Constructs 3D protein structures based on homologous templates.</li>
<li class="resource-item"><strong><a href="https://swissmodel.expasy.org/" target="_blank">Swiss-Model:</a></strong> Automates template selection and homology-based structure modeling.</li>
<li class="resource-item"><strong>Model Evaluation and Energy Minimization:</strong></li>
<li class="resource-item"><strong><a href="http://www.yasara.org/" target="_blank">YASARA:</a></strong> Performs energy minimization and molecular simulations.</li>
<li class="resource-item"><strong><a href="http://saves.mbi.ucla.edu/" target="_blank">SAVES:</a></strong> Assesses stereochemistry and structure validation of protein models.</li>
<li class="resource-item"><strong><a href="http://superpose.wishartlab.com/" target="_blank">Superpose:</a></strong> Compares 3D structural alignments of proteins.</li>
<li class="resource-item"><strong>Active Site Prediction:</strong></li>
<li class="resource-item"><strong><a href="http://pockdrug.loria.fr/" target="_blank">POCKDRUG:</a></strong> Identifies and characterizes ligand-binding pockets.</li>
<li class="resource-item"><strong><a href="https://discover.3ds.com/products/discovery-studio/visualizer" target="_blank">Biovia Discovery Studio Visualizer:</a></strong> Analyzes and visualizes molecular interactions.</li>
<li class="resource-item"><strong>Ligand Design:</strong></li>
<li class="resource-item"><strong><a href="https://chemaxon.com/products/marvin" target="_blank">Marvin JS:</a></strong> Facilitates chemical structure drawing and editing.</li>
<li class="resource-item"><strong>Pharmacophore Modeling and Virtual Screening:</strong></li>
<li class="resource-item"><strong><a href="https://www.eyesopen.com/ligandscout" target="_blank">LigandScout:</a></strong> Generates pharmacophore models for drug discovery.</li>
<li class="resource-item"><strong><a href="https://www.zincpharmer.com/" target="_blank">ZINCPHARMER:</a></strong> Screens ligand databases for potential drug candidates.</li>
<li class="resource-item"><strong>Pharmacodynamics and ADMET Analysis:</strong></li>
<li class="resource-item"><strong><a href="http://www.swissadme.ch/" target="_blank">SwissADME:</a></strong> Predicts pharmacokinetics and drug-likeness of molecules.</li>
<li class="resource-item"><strong><a href="http://admet.sct.su.ac.th/" target="_blank">ADMETSAR-2.0:</a></strong> Evaluates absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.</li>
<li class="resource-item"><strong>Molecular Docking:</strong></li>
<li class="resource-item"><strong><a href="http://vina.scripps.edu/" target="_blank">AutoDock Vina:</a></strong> Performs ligand-protein docking simulations.</li>
<li class="resource-item"><strong><a href="http://bioinfo3d.cs.toronto.edu/patchdock/" target="_blank">PatchDock:</a></strong> Conducts molecular docking through geometric shape complementarity.</li>
<li class="resource-item"><strong><a href="http://firedock.loria.fr/" target="_blank">FireDock:</a></strong> Refines docking results with energy-based optimization.</li>
<li class="resource-item"><strong>Molecular Dynamics Simulation:</strong></li>
<li class="resource-item"><strong><a href="http://www.gromacs.org/" target="_blank">GROMACS:</a></strong> Runs high-performance molecular dynamics simulations.</li>
<li class="resource-item"><strong>Analysis of MD Trajectories:</strong></li>
<li class="resource-item"><strong><a href="http://www.ks.uiuc.edu/Research/vmd/" target="_blank">VMD:</a></strong> Visualizes and analyzes molecular dynamics trajectories.</li>
<li class="resource-item"><strong>Pocket Dynamics Analysis:</strong></li>
<li class="resource-item"><strong><a href="http://trapp.kaust.edu.sa/" target="_blank">TRAPP Web Server:</a></strong> Studies the dynamic behavior of binding pockets.</li>
<li class="resource-item"><strong>Density Functional Theory (DFT) Calculation:</strong></li>
<li class="resource-item"><strong><a href="https://www.wavefunction.com/products/spartan/" target="_blank">Spartan 14:</a></strong> Computes electronic properties like HOMO/LUMO analysis.</li>
<li class="resource-item"><strong>Protein Annotation and Functional Prediction:</strong></li>
<li class="resource-item"><strong><a href="http://pfam.xfam.org/" target="_blank">Pfam:</a></strong> Detects conserved protein families and domains.</li>
<li class="resource-item"><strong><a href="http://www.cbs.dtu.dk/services/SignalP/" target="_blank">SignalP:</a></strong> Predicts signal peptides for protein secretion.</li>
<li class="resource-item"><strong>Epitope Prediction and Vaccine Design:</strong></li>
<li class="resource-item"><strong><a href="http://tools.iedb.org/main/" target="_blank">IEDB Tools:</a></strong> Identifies MHC-binding and B-cell epitopes for vaccine design.</li>
<li class="resource-item"><strong>Codon Optimization and In-Silico Cloning:</strong></li>
<li class="resource-item"><strong><a href="https://www.snapgene.com/" target="_blank">SnapGene:</a></strong> Simulates in-silico DNA cloning and plasmid construction.</li>
<li class="resource-item"><strong>mRNA Structure Prediction:</strong></li>
<li class="resource-item"><strong><a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi" target="_blank">RNAfold:</a></strong> Predicts secondary structures of RNA sequences.</li>
</ul>
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