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Useful Links

CompChem Sites

CCDB: CompChem Databases
HPC: CompChem-HPC Monitoring
Winsoftware: Windows Software
Files: CompChem Files

Typing Software

SpeedTyping: Speed Typing Online

Visualization Software

Jalview: Jalview is a free program for multiple sequence alignment editing, visualization and analysis
CASTp: CASTp: Computed Atlas of Surface Topography of proteins

Linux Tutorials

Basic Commands: Basic Linux Commands for Beginners

Gaussian Tools

NIST Database: Precomputed vibrational scaling factors
Basis Set Exchange: All basis sets

Pharmacokinetic Properties

pkCSM: Prediction of Pharmacokinetic Properties
Molinspiration: Calculation of Molecular Properties and Bioactivity Score
AdmetSAR: Prediction of ADME profiles, toxicity and the drug-likeness
Protox II: Prediction of toxicity

Cheminformatics

Interactivenn: Venn Diagram
PPI: Protein-Protein Interaction
STRING: String for PPI

Drug Discovery Tools

Pharmit: interactive exploration of chemical space (Pharmacophore Virtual Screening)
CLUE: Drug repurposing hub
SIDER4.1: Side Effect Resource
SuperPred: Predicting ATC codes or targets of small molecules
CovalentInDB: Covalent Inhibitor Database
Classyfire: Web-based application for automated structural classification of chemical entities
SwissBioisostere: An online server to explore possible Bioisosteric replacements in lead optimization
Ochem: Online modeling environment for creating and applying QSAR models and calculate descriptors
PharmaGist: Program used to extract pharmacophore from given set of compounds
SmiLib: Java based tool to generate combinatorial compounds from given set of fragments
LigDream: Generation of novel compounds through generative shape-based neural network decoding
PrankWeb: Ligand Binding Site Prediction
IUPred3: Prediction of Intrinsically Unstructured Proteins
drugvirus: Drug-Virus Information
TTD: Therapeutic target database
NPBS: Natural product and biological source
AVCPRED: a web based algorithm for prediction and design of antiviral compounds

Materials Project

MaterialsProject: Website for materials projects

Online Tools

WebPlotDigitizer: Website for extracting XY data from figure

NMR Tools

CHESHIRE: Chemical Shift Repository for computed NMR scaling factors, with Coupling Constants Added Too

DNA/RNA Tools

DSSR: DSSR-enabled Innovative Schematics of 3D Nucleic Acid Structures with PyMOL
VARNA: Visualization Applet for RNA
3DNA: Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures
HNADock: Nucleic acid (NA) docking for RNA/DNA-RNA/DNA complex structure modeling
3D-NuS: Automated Modeling and Visulations of 3 Dimentaion Nucleic Acid Structures

Protein-Protein Docking and Scoring

DockScore: Scoring Server for docked poses
HawkDock: A web server for the structural prediction and analysis of protein-protein complex

Peptides Databases

BioPepDB: Repository of bioactive peptides
PeptideDB: Bioactive peptide database
AHTPDB: Anti Hypertensive Inhibiting peptide database
PeptaibolDB: Peptaibol Database
BaAMPs: Biofilm-active antimicrobial peptides database
BactPepDB: Bacterial peptides database
BactiBase: Bacterial antimicrobial peptides
Brainpeps: Blood-brain barrier properties of peptides
DADP: Database of Anuran Defense Peptides
InverPep: Database of antimicrobial peptides from invertebrates Peptides
LAMP2: Updated linking antimicrobial peptide database
KaliumDB: Database of polypeptide ligands of potassium channels
NeuroPedia: Neuropeptides are essential peptides for cell-cell communication in neurological and endocrine physiological processes in health and disease
FermFooDB: Database of peptides derived from fermented foods
NeuroPep: a Comprehensive Resource of Neuropeptides
PepBank: a a database of peptides based on sequence text mining and public peptide data sources
ProPedia: A database of peptide-protein interactions
StraPep: Structure database of Bioactive Peptides
YADAMP: yet another database of antimicrobial peptides
NORINE: A database of nonribosomal peptides
CancerPDF: database of cancer-associated peptides found in different human bodyfluids
THPdb: A comprehensive database based on approved and approved/investigational therapeutic peptides compiling important information about these peptides
CAMP(R3): Collection of Anti-Microbial Peptides
Bcipep: A database of B-cell epitopes
CPPsite: Database of cell penetrating peptides
DBAASP: Database of Antimicrobial Activity and Structure of Peptides
APD3: Antimicrobial peptide database
PepBDB: A structural database of biological peptide-mediated interactions
MBPDB: Milk Bioactive Peptide database
ConoServer: A database for conopeptides
AntiTbPdb: Anti Tubercular Peptide Database