Molecular Docking Service

Molecular docking is a computational method that predicts the preferred binding orientation of one molecule to another when bound to form a stable complex. At Lakshmi Biosciences, we employ both rigid and flexible docking protocols using Glide (Schrödinger), AutoDock Vina, HADDOCK, and HDOCK to deliver accurate binding pose predictions and energy scoring.

Service Offerings

• Protein-Small Molecule (Ligand) Docking
• Protein-Protein Docking (PPI studies)
• Protein-Peptide Docking
• Protein-DNA Docking
• Protein-RNA Docking
• Antibody-Antigen Docking
• Covalent Docking
• Ensemble Docking
• Induced-Fit Docking (IFD)

Software & Tools

• Glide (Schrödinger Suite) — SP, XP, IFD modes
• AutoDock Vina & AutoDock 4
• HADDOCK (protein-protein)
• HDOCK, PatchDock, ClusPro
• Discovery Studio for 2D interaction analysis

Deliverables

• Top-ranked docking poses (PDB/MOL2 files)
• Binding energy / docking score tables
• 2D & 3D interaction diagrams
• Hydrogen bond, hydrophobic, and π-interaction analysis
• Publication-ready molecular visualization figures
• Comprehensive docking report (PDF)

Molecular Dynamics Simulation

Molecular dynamics (MD) simulation is a powerful technique for studying the physical movements of atoms and molecules over time. Our MD simulations provide atomic-level insights into protein conformational changes, protein-ligand binding stability, membrane protein behavior, and thermodynamic properties crucial for drug discovery.

Service Offerings

• Protein MD Simulation (explicit/implicit solvent)
• Protein-Ligand Complex MD Simulation
• Lipid Bilayer MD Simulation
• Membrane Protein MD Simulation
• Protein-Protein Complex MD Simulation
• GPCR MD Simulation
• Enhanced Sampling MD (metadynamics, replica exchange)
• Free Energy Perturbation (FEP) Calculations
• Binding Free Energy (MM-GBSA / MM-PBSA)

Software Used

• GROMACS (versions 2020–2023)
• AMBER & AMBER MD
• NAMD / CHARMM
• Desmond (Schrödinger Suite)
• VMD & PyMOL for trajectory analysis & visualization

Deliverables

• RMSD, RMSF, Rg trajectory plots
• H-bond occupancy analysis
• MM-GBSA binding free energy values
• Principal Component Analysis (PCA)
• Simulation trajectory files
• Full MD simulation report (PDF)

Virtual Screening Service

Virtual screening (VS) is a key component of computer-aided drug discovery that enables rapid screening of large compound databases to identify novel drug candidates. We offer both structure-based (SBVS) and ligand-based (LBVS) virtual screening workflows using curated chemical databases including ZINC, ChEMBL, PubChem, and custom client libraries.

Service Offerings

• Structure-Based Virtual Screening (SBVS)
• Ligand-Based Virtual Screening (LBVS)
• High-Throughput Virtual Screening (HTVS)
• Pharmacophore-Based Virtual Screening
• ADMET-Filtered Screening
• Fragment-Based Virtual Screening
• Covalent Drug Virtual Screening
• Multiple-Target Virtual Screening
• Natural Product Library Screening

Deliverables

• Top-ranked hit list with docking scores and ADMET profiles
• Binding pose visualization for top hits
• Interaction fingerprint analysis
• Drug-likeness and Lipinski's Rule of Five compliance
• Full virtual screening report (PDF)

Molecular Modeling Service

Molecular modeling encompasses computational techniques to generate, manipulate, and analyze 3D models of molecules. Our team builds accurate structures for diverse biomolecular systems including proteins, antibodies, peptides, small molecules, carbohydrates, and metal complexes to support drug discovery and structural biology research.

Service Offerings

• Protein Structure Modeling (Homology, AlphaFold, RoseTTAFold)
• Virtual Cell Modeling
• Antibody Modeling (VH/VL domain modeling)
• Peptide Modeling (linear, cyclic, signal peptides)
• Small Molecule 3D Structure Generation & Optimization
• Natural Product Modeling
• Metal Complex Modeling
• Inhibitor Modeling
• Carbohydrate / Glycan Modeling

Deliverables

• 3D structure files (PDB, MOL2, SDF formats)
• Structure quality assessment (PROCHECK, ERRAT, VERIFY3D)
• Ramachandran plot analysis
• Energy minimized structures
• Publication-ready structural figures

Drug Discovery & Design Service

Lakshmi Biosciences provides comprehensive computer-aided drug design (CADD) services integrating structure-based and ligand-based approaches to design and optimize drug candidates with improved potency, selectivity, and drug-like properties across diverse modalities.

Service Offerings

• Small Molecule Drug Design
• Protein Drug Design
• Peptide Drug Design
• DNA / RNA Drug Design
• Cytokine Drug Design
• Enzyme Drug Design
• Protein Vaccine Design
• Antibody Drug Design (Monoclonal, Bispecific, Single Domain, Polyclonal)
• Antibody De Novo Design
• Drug Target Identification & Validation
• Drug Repositioning / Repurposing
• Drug Interaction & Structure Analysis
• Drug Optimization & Modification Simulation

Deliverables

• Designed drug candidate structures
• Structure-activity relationship (SAR) analysis
• ADMET profile of candidates
• Binding mode and interaction analysis report
• Lead optimization recommendations

Targeted Protein Degradation Service

Targeted protein degradation (TPD) is a revolutionary approach leveraging the cell's own ubiquitin-proteasome system to eliminate disease-causing proteins. Our team specializes in computational design of PROTACs (proteolysis-targeting chimeras), KineTACs, and LYTACs using state-of-the-art modeling tools.

Service Offerings

• PROTAC Design & Optimization
• PROTAC Linker Design & Length Optimization
• E3 Ligase Ligand Design (CRBN, VHL, MDM2)
• PROTAC Structure Analysis & Profiling
• KineTACs Design and Development
• LYTACs Design and Development
• Ternary Complex Modeling
• Cooperativity Analysis
• ADMET profiling of PROTAC molecules

Deliverables

• Designed PROTAC / KineTAC / LYTAC structures
• Ternary complex docking models
• Linker length and composition analysis report
• E3 ligase binding analysis
• ADMET and drug-likeness assessment

Computational Pharmacology Service

Computational pharmacology combines pharmacological principles with advanced computational methods to predict drug behavior in biological systems. Our services help accelerate early drug development by identifying problematic ADMET properties before costly laboratory experiments.

Service Offerings

• In Silico ADMET Prediction
• Physicochemical Property Prediction (LogP, pKa, solubility, MW)
• Pharmacological Analysis & Modeling
• Computational PK/PD Modeling
• Toxicity Prediction (Ames, mutagenicity, carcinogenicity)
• Blood-Brain Barrier (BBB) Permeability Prediction
• hERG Cardiotoxicity Prediction
• Metabolic Stability Analysis (CYP450 interactions)
• Oral Bioavailability Prediction

Deliverables

• ADMET profile report for each compound
• Physicochemical property summary table
• Lipinski's Rule of Five & Veber's Rule analysis
• Toxicophore identification and flagging
• Bioavailability radar charts
• Comprehensive pharmacology report (PDF)

Bioinformatics & Multi-Omics Service

Our bioinformatics team provides cutting-edge multi-omics data analysis services to uncover molecular mechanisms of disease, identify biomarkers, and support translational research from bench to clinic. We integrate genomics, transcriptomics, proteomics, and metabolomics data for a holistic view of biological systems.

Service Offerings

• Genomics — DNA Modification & Variant Analysis
• Epigenomics — Histone & DNA Methylation Analysis
• Transcriptomics — mRNA, microRNA, lncRNA Analysis
• Proteomics — Protein Structure, PTM, and Expression Analysis
• Metabolomics — Metabolic Flux and Pathway Analysis
• Lipidomics Analysis
• Glycomics Analysis
• Nucleotide Sequence Analysis
• Integrated Multi-Omics Analysis
• Single-Cell Omics (scRNA-seq, scATAC-seq)
• Network Analysis & Pathway Enrichment

Deliverables

• Omics data analysis reports with statistical outputs
• Pathway and gene ontology (GO) enrichment analysis
• Differential expression analysis results
• Network and heatmap visualizations
• Biomarker identification summary
• Publication-ready figures (volcano plots, PCA, heatmaps)

Computational Chemistry Service

Our computational chemistry team uses quantum mechanical methods and molecular mechanics to study chemical properties, reaction mechanisms, and spectroscopic characteristics of organic and inorganic compounds, natural products, and drug molecules.

Service Offerings

• Quantum Chemistry Calculations (DFT, HF, MP2, CCSD)
• Chemical Property Calculations (HOMO-LUMO, ESP, NBO, FMO)
• NMR Spectrum Prediction (¹H, ¹³C, COSY, HSQC, HMBC)
• IR Spectrum Prediction
• UV-Vis Spectrum Prediction
• ECD (Electronic Circular Dichroism) Prediction
• VCD (Vibrational Circular Dichroism) Prediction
• ROA (Raman Optical Activity) Prediction
• Fluorescence Spectrum Prediction
• Phosphorescence Prediction
• Specific Rotation Calculation
• Reaction Mechanism Study (transition state, IRC)

Software Used

• Gaussian 16 / G09 — DFT, HF, MP2, TDDFT
• ORCA — High-accuracy single-point calculations
• NWChem, ADF (Amsterdam Density Functional)
• GaussView 6 for molecular visualization

Data Science & Biostatistics Service

Our data science and biostatistics team provides comprehensive analytical support for biological and clinical research, applying advanced statistical methods and AI-driven approaches to extract meaningful insights from complex datasets in genomics, clinical trials, and drug discovery.

Service Offerings

• Biological Data Analysis
• Statistical Analysis (parametric & non-parametric)
• Clinical Data Analysis & Reporting
• Survival Analysis (Kaplan-Meier, Cox regression)
• Protein Sequence Analysis
• Network Biology Analysis
• Disease Research Support
• Compound Library Design & Clustering
• Database Mining (PubChem, ChEMBL, DrugBank, UniProt)
• Machine Learning for Drug Discovery
• AI-Powered Biomarker Discovery

Deliverables

• Statistical analysis reports with p-values & effect sizes
• Publication-ready data visualizations (volcano plots, PCA, heatmaps)
• Network topology analysis results
• Clinical data summary tables
• R / Python scripts for reproducible analysis

Structural Bioinformatics Service

Structural bioinformatics integrates computational methods with structural data to understand the relationship between macromolecular structure and function. Our services bridge protein structure analysis with rational drug design, providing detailed structural insights for target characterization and drug development.

Service Offerings

• Protein Structure Prediction (AlphaFold2, RoseTTAFold, ESMFold)
• Structure-Based Drug Design (SBDD)
• Binding Site Identification & Analysis
• Pocket Druggability Assessment
• Protein-Protein Interaction (PPI) Analysis
• Allosteric Site Identification
• Comparative Structural Analysis
• Protein Stability Analysis (thermostability prediction)
• Macromolecular Complex Structure Analysis

Deliverables

• Predicted protein structures (PDB format)
• Binding site maps and druggability scores
• Structural superimposition and RMSD analysis
• Contact map analysis
• Publication-ready PyMOL visualization images

Drug Development & Optimization Service

Lakshmi Biosciences provides computational support across the entire drug development pipeline — from early-stage target identification and hit finding to lead optimization and preclinical candidate selection. We integrate structure-based and ligand-based methods with predictive ADMET profiling.

Service Offerings

• Drug Discovery — Target Identification & Validation
• Hit Identification via Virtual Screening
• Lead Optimization (SAR studies)
• Drug Repositioning / Repurposing
• Preclinical Candidate Selection Support
• Drug Interaction & Selectivity Analysis
• Multi-Parameter Optimization (MPO)
• Medicinal Chemistry-Guided Modification
• ADMET-Guided Lead Optimization

Deliverables

• Hit-to-Lead optimization report
• SAR analysis summary
• Optimized lead candidate structures
• ADMET and drug-likeness profiles
• Comparative binding analysis

Research Support

Lakshmi Biosciences offers comprehensive research support services to help scientists, scholars, and institutions communicate their work effectively and navigate the publication and IP landscape. From first draft to final submission, our team combines subject-matter expertise with scientific writing and editorial precision.

Service Offerings

• Manuscript Writing & Editing
• Systematic Reviews & Meta-Analysis
• Grant & Patent Proposal Writing
• Scientific Visualization & Design
• Literature Review Compilations
• Patent Landscape Analysis
• Graphical Abstract Prototyping
• Bioinformatics Training & Consulting
• Journal Response Coordination
• Peer-Review Validation Screening

Deliverables

• Submission-ready manuscript draft
• Comprehensive literature review report
• Polished grant/patent proposal document
• Publication-quality graphical abstracts & figures
• Point-by-point peer-review response letters