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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.

In investigations of biological features and 'living systems' we try to follow the approaches of Izrael Gelfand, the organizer of the Department.

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
  • Ccalc — estimated/observed frequencies of words in a genetic text
  • PQ — phylogenetic reconstruction
  • Mini tools

Protein families

Other projects


Bioinformatics portal of A.N.Belozersky Institute

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