Guides & research, page 2

In-depth guides on protein analysis, molecular docking, drug discovery, and bioinformatics tools.

Genetics · 18 min
Phylogenetic tree: what it shows and how to read one
A phylogenetic tree is a hypothesis about how sequences or species descend from common ancestors. Learn the parts of a tree, how to read relatedness from common ancestors rather than tip order, rooted vs unrooted trees, cladograms, phylograms and chronograms, bootstrap and UFBoot support, the Newick format, and common misreadings, with a real primate tree built from nine mitochondrial genomes.
Proteins · 19 min
Post-translational modifications: types, examples and what they do
Post-translational modifications (PTMs) are covalent changes to a protein during or after its synthesis: phosphorylation, glycosylation, acetylation, methylation, ubiquitination, SUMOylation, lipidation, proteolytic cleavage, disulfide bonds and hydroxylation. Learn which residues each one targets, where in the cell it happens, how common it is in UniProtKB/Swiss-Prot, how it changes charge, mass, localization, stability and activity, and how mass spectrometry detects it.
Genetics · 18 min
Primer dimers: how they form, how to predict them and how to stop them
A primer dimer is a short PCR artifact made when two primers anneal to each other and the polymerase extends them. Learn why 3′ complementarity matters most, how dimers show up on gels, melt curves and no-template controls, how ΔG and Primer3's complementarity limits score them, and how to prevent and fix them, with a worked β-actin example.
Proteins · 16 min
Protein aggregation: causes, prediction and prevention
Protein aggregation is the self-association of protein molecules into amorphous clumps, soluble oligomers or ordered amyloid fibrils. Learn why proteins aggregate, how aggregates are measured, what TANGO, AGGRESCAN, CamSol, Aggrescan3D, Protein-Sol and NetSolP predict from sequence and structure, and how formulation, mutations and expression conditions prevent it, with a worked Aggrescan3D run on transthyretin.
Proteins · 17 min
What is protein denaturation?
Protein denaturation is the loss of a protein's secondary, tertiary and quaternary structure while its amino acid sequence and peptide bonds stay intact. Learn how heat, cold, pH, urea, SDS, alcohol and force unfold proteins, why most proteins are stable by only 5 to 15 kcal/mol, why Anfinsen's ribonuclease refolds but egg white does not, and how CD, fluorescence, DSC and DSF measure it.
Proteins · 16 min
Protein extinction coefficient and A280 concentration
The molar extinction coefficient converts a protein's absorbance at 280 nm into a concentration through the Beer-Lambert law. It is predicted from the number of tryptophans, tyrosines and disulfide bonds with the Pace equation, which is reliable to a few percent for proteins with tryptophan and less so for proteins without it. Learn the mass and molar forms, a worked A280 example, and when A280 gives the wrong answer.
Proteins · 16 min
Isoelectric point of a protein: what pI means and how it is calculated
The isoelectric point (pI) is the pH at which a protein carries zero net charge. Learn how calculators find it from the sequence, why EMBOSS, ExPASy (Bjellqvist), Lehninger and IPC 2.0 give different values, how pI is distributed across the human proteome, and how to use it for isoelectric focusing, ion exchange and solubility.
Proteins · 17 min
What is a protein language model, and what is it used for
A protein language model is a neural network trained to predict amino acids from the rest of a sequence. Learn how ESM-2, ESM C, ESM3, ProtT5 and ProGen2 differ, what their embeddings and likelihoods are used for, how they compare with alignment-based methods like AlphaFold2, and which licences allow commercial use.
Genetics · 16 min
RNA secondary structure: dot-bracket notation and MFE explained
RNA secondary structure is the set of base pairs an RNA strand forms with itself: stems, hairpins, bulges, internal loops and multiloops. Learn how dot-bracket notation encodes it, what the minimum free energy (MFE) means in the nearest-neighbor model, and how accurate thermodynamic prediction is.
Drugs · 20 min
SDF file format: how SDF and MOL files work
An SDF (structure-data file) stores one or more small molecules as MDL molfiles, each followed by named data fields and a line of four dollar signs. Learn the molfile layout line by line, V2000 vs V3000, 2D vs 3D records, and how SDF compares with MOL2 and PDBQT for docking.
Drugs · 18 min
SMILES notation: how to read and write SMILES strings
SMILES (Simplified Molecular Input Line Entry System) writes a molecule's atoms and bonds as one line of text, such as CC(=O)Oc1ccccc1C(=O)O for aspirin. Learn the grammar with worked drug examples, how @, @@, / and \ encode stereochemistry, why canonical SMILES differ between databases, and how SMILES compares with InChI and SELFIES.
Antibodies · 10 min
How many bispecific antibodies are approved?
By our count of agency records, 25 bispecific antibodies had been approved by the FDA, the EU, China or Japan by October 29, 2026. The FDA had approved 15, the EU 16, China 17 and Japan 12.
Drugs · 15 min
How many covalent drugs are approved?
A covalent drug forms a chemical bond with its target. ProteinIQ checked 2,104 approved small-molecule drugs in ChEMBL 37 and found 173 that act this way, 8.2% of the set, and 36 (1.7%) that were designed as targeted covalent drugs. Published counts of 50 to 128 differ mainly in whether beta-lactams and DNA alkylators are included.
Drugs · 14 min
How many oligonucleotide drugs are approved?
The FDA has approved 25 oligonucleotide drugs since 1998, and 21 are still sold in the US. Adding Europe and Japan gives 26. Full list of antisense, siRNA and aptamer drugs with a free CSV, checked October 29, 2026.
Drugs · 14 min
How many radiopharmaceutical therapies are approved?
The FDA has approved 11 radiopharmaceutical therapies since 1957, and 6 are approved today. Lutetium-177 dotatate gained two copies in September 2026. ClinicalTrials.gov lists 1,041 therapy trials, led by lutetium-177. Full list and CSVs, checked October 29, 2026.
Structures · 12 min
What clashscore means and what counts as good
Clashscore is the number of serious all-atom overlaps, 0.4 Å or more, per 1,000 atoms of a structure. See what counts as a clash, typical values by resolution across 112,000 PDB entries, and how to fix a high score.
Drugs · 13 min
How many drug targets are there?
ProteinIQ counted 809 molecular targets behind 2,205 approved drugs in ChEMBL 37: 611 in humans and 179 in pathogens. GPCRs carry 22% of those drugs; the often quoted 34% uses a smaller FDA list.
Antibodies · 12 min
How many antibody-drug conjugates are FDA approved?
The FDA has approved 15 antibody-drug conjugates, and all 15 are licensed today, including Mylotarg and Blenrep, which were withdrawn and later re-approved. Adding Europe and China gives 21. Full list and CSV, checked October 29, 2026.
Drugs · 16 min
How many peptide drugs are FDA approved?
The FDA has approved 98 peptide drugs of 2 to 50 amino acids, and 77 are still marketed in the US. Leaving out antibiotics made by microbes gives 79; adding the insulins gives 106. Full list, GLP-1 family and free CSV, checked October 29, 2026.
Docking · 15 min
GNINA CNN score vs CNN affinity: what each number means
GNINA's CNN pose score is the probability that a docked pose lies within 2 Å of the true pose. CNN affinity is a predicted pK, and the empirical score is a Vina-style kcal/mol value. Learn how to read, threshold and combine them.
Genetics · 12 min
How much DNA do humans share with pigs?
Not 98%. About half of the human genome aligns with pig DNA, aligned coding letters match at 86.7%, and a typical pig protein is 89.1% identical to the human one, against 99.3% for chimpanzees.
Antibodies · 12 min
Human vs humanized vs chimeric antibodies: the origin of every FDA-approved antibody
Of 159 antibody products the FDA licensed by September 2026, 52% are humanized, 34% fully human, 9% chimeric and 5% murine, by ProteinIQ's label-by-label count. The fully human share has held near one-third since 2015. Free CSV.
Drugs · 14 min
IC50 vs Ki vs Kd: what each measures and how to convert them
IC50 is the inhibitor concentration that halves activity in one assay. Ki and Kd are equilibrium dissociation constants that do not depend on the assay. Learn how the Cheng-Prusoff equation converts IC50 to Ki, when it fails, and why potency is compared as pIC50.
Drugs · 14 min
Lipinski's rule of five
Lipinski's rule of five warns that oral absorption is less likely when a molecule breaks two or more of four limits: molecular weight above 500 Da, cLogP above 5, more than 5 hydrogen-bond donors and more than 10 acceptors. ProteinIQ found that 13% of 2,104 approved small-molecule drugs in ChEMBL 37 break two or more, and 28% break at least one.

Phylogenetic tree: what it shows and how to read one

Post-translational modifications: types, examples and what they do

Primer dimers: how they form, how to predict them and how to stop them

Protein aggregation: causes, prediction and prevention

What is protein denaturation?

Protein extinction coefficient and A280 concentration

Isoelectric point of a protein: what pI means and how it is calculated

What is a protein language model, and what is it used for

RNA secondary structure: dot-bracket notation and MFE explained

SDF file format: how SDF and MOL files work

SMILES notation: how to read and write SMILES strings

How many bispecific antibodies are approved?

How many covalent drugs are approved?

How many oligonucleotide drugs are approved?

How many radiopharmaceutical therapies are approved?

What clashscore means and what counts as good

How many drug targets are there?

How many antibody-drug conjugates are FDA approved?

How many peptide drugs are FDA approved?

GNINA CNN score vs CNN affinity: what each number means

How much DNA do humans share with pigs?

Human vs humanized vs chimeric antibodies: the origin of every FDA-approved antibody

IC50 vs Ki vs Kd: what each measures and how to convert them

Lipinski's rule of five