Multiple flexible protein structure alignments (2019)
Kpax is a fast protein structure alignment and database search program. It uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it uses dynamic programming to find the optimal global alignment and superpositions of two proteins according to their Gaussian similarity scores.
Context-dependant databases and libraries of protein-bound RNA fragments (2020)
NAfragDB is a modular tool to create customized selections of RNA-protein structures from the PDB, extract biological and structural information, embed it into a database, and create structural libraries of RNA fragments of givens characteristics (sequence, size, 2D structure, bound protein family…)
fragment-based docking of ssRNA in deep protein cavities (2018)
High order Clebsch-Gordan coupling coefficients (2018)
CGC is a small C library and a test program for calculating high order Clebsch-Gordan coupling coefficients. Here, high order means principal quantum numbers of up to about 260 in ordinary double precision and 400 or more in long double precision. When using the GMP arbitrary precision math library, there is essentially no limit on the maximum quantum numbers. The code was written by Dave Ritchie.
Database of protein domain-domain interactions (2016)
KBDOCK is a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK combines the PFAM domain classification with coordinate data from the PDB to analyse the spatial arrangements of domain-domain interactions (DDIs) and domain-peptide interactions (DPIs) by Pfam family, and to propose structural templates for protein docking.
Protein symmetry assembler using spherical polar FFT (2015)
Sam is a fast FFT-based protein docking program that has been specifically designed to assemble perfectly symmetrical protein complexes with arbitrary point group symmetry.
Sam was developed by Dave Ritchie and Sergei Grudinin.
cryo-EM particle picking and 3D density fitting (2014)
gEMtools – a collection of programs for processing cryo-electron microscopy (« cryo-EM ») datasets. gEMtools suite uses fast Fourier transform (FFT) correlation techniques to accelerate the calculations, and it uses parallel processing techniques to distribute the FFT calculations over multiple CPU cores in a workstation and multiple nodes in a computer cluster. A particular novelty of the gEMtools programs is that they can use multiple graphics processor units (GPUs) to accelerate the correlation calculations even further.
Ultra-fast protein-protein docking using spherical polar FFT (2013)
Hex is an interactive protein docking and molecular superposition program, written by Dave Ritchie.
Associating Pfam domains with enzyme EC numbers
ECDomainMiner, a novel content-based filtering approach to automatically infer associations between EC numbers and Pfam domains. ECDomainMiner finds a total of 20,728 non-redundant EC-Pfam associations with a F-measure of 0.95 with respect to a “Gold Standard” test set extracted from InterPro. Compared to the 1515 manually curated EC-Pfam associations in InterPro, ECDomainMiner infers a 13-fold increase in the number of EC-Pfam associations.
Currently Not Maintained
– Gene Ontology semantic similarity measure
This article is about IntelliGO.
– FFT-based protein shape comparison
– Small molecule virtual drug screening
This chapter is about Spherical Harmonic Molecular Surfaces (Parasurf and Parafit).