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Structures and Sequences

The page of the interdisciplinary seminar/working group based on the Department of Mathematical Methods in Biology of A.N. Belozersky Institute, Moscow State University.

Our projects

Data Base

• NPIDB — a database of structures of DNA-protein and RNA-protein complexes.
• Old version of NPIDB
• PLANdbAffy — a probe-level annotation database for Affymetrix expression microarrays.

Tools

• CluD — a program for finding hydrophobic clusters in 3D structures of macromolecules
• ConClus — search of conserved hydrophobic clusters in aligned 3D structures of protein families
• SVETKA — a program for analysis of multiple alignments
• Nhunt — a program for search nucleotide database using nucleotide query
• NPG-explorer — a tool for aligning multiple genomes of closely related prokaryotes
• plot-hits — a tool for simultaneous vizualization of annotated genes and blast-hits in contigs of de novo genome assembly and annotation
• wLake — a program for detecting structural water molecules
• MALAKITE — a program for automatic detection of aligned blocks in a multiple protein alignment.
• Blocks_3d/pair-cores — a program for detection of aligned blocks in a multiple alignment of sequences of PDB chains.
• ProtOn — tools for automatic description of all-β and α/β protein structures, include detectors of β-sheets, architectures and structural motifs.
• Gcore — geometrical core for a family of protein 3D structures
• Lcore — geometrical core for a family of 3D structures of macromolecular complexes
• StructAlign — structural alignment of two complexes of protein with double-stranded DNA
• MTpro — automatic classification of an input sequence of DNA methyltransferase according to classification by methylation type, motif sequence and restriction-modification system type
• Mini tools

Protein families

Other projects

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