Protein structure

Foldit is an online puzzle video game about protein folding.

Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences.

In biochemistry and structural biology, protein secondary structure is the general three-dimensional form of local segments of proteins.

A dihedral angle is the angle between two intersecting planes.

Folding@home (FAH or F@h) is a distributed computing project for disease research that simulates protein folding, computational drug design, and other types of molecular dynamics.

Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat.

Ubiquitin is a small (8.5 kDa) regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms.

Rosetta@home is a distributed computing project for protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker laboratory at the University of Washington.

The term protein tertiary structure refers to a protein's geometric shape.

Intelectins are lectins (carbohydrate-binding proteins) expressed in humans and other chordates.

WHAT IF is a computer program used in a wide variety of computational (in silico) macromolecular structure research fields.

Voltage sensitive phosphatases or voltage sensor-containing phosphatases, commonly abbreviated VSPs, are a protein family found in many species, including humans, mice, zebrafish, frogs, and sea squirt.

Caspase recruitment domains, or Caspase activation and recruitment domains (CARDs), are interaction motifs found in a wide array of proteins, typically those involved in processes relating to inflammation and apoptosis.

In chemistry and biology a disulfide refers to a functional group with the general structure R–S–S–R'.

The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein interactions for which a high-resolution 3D structure is known.

The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences.

There are very few loops registered in Brix, so to address this issue, Loop Brix was added to the system to help structure non-regular elements.

geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis.

The Biomolecule Stretching Database contains information about the mechanostability of proteins based on their resistance to stretching.

The L27 domain is a protein domain that is found in receptor targeting proteins Lin-2 and Lin-7 (LIN7A, LIN7B, LIN7C), as well as some protein kinases and human MPP2 protein.

Nucleotide pyrophosphatase/phosphodiesterase (NPP) is a class of dimeric enzymes that catalyze the hydrolysis of phosphate diester bonds.

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence.

Guanidinium chloride or guanidine hydrochloride, usually abbreviated GdmCl and sometimes GdnHCl or GuHCl, is the hydrochloride salt of guanidine.

The Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains.

The Protein Common Interface Database (ProtCID) is a database of similar protein-protein interfaces in crystal structures of homologous proteins.

Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids.

A cystine knot is a protein structural motif containing three disulfide bridges (formed from pairs of cysteine residues).

ModBase is developed in the laboratory of Andrej Sali at UCSF.

X-ray crystallography is a tool used for identifying the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.

Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes.

Circular dichroism (CD) is dichroism involving circularly polarized light, i.

Analysis is carried out by coarse-grained computation of the structures present in the electron microscopy data bank (EMDB).

Conformational entropy is the entropy associated with the number of conformations of a molecule.

SHIFTCOR (Shift Correction) is a freely available web server as well as a stand-alone computer program for protein chemical shift re-referencing.

Arthur Mallay Lesk, is a protein science researcher, who is a professor of biochemistry and molecular biology at the Pennsylvania State University in University Park.

The name CATH is an acronym of the four main levels in the classification.

The Conserved Domain Database (CDD) is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins.

The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography.