We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures, as well as on a set low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA

A procedure for the reconstruction of all‐atom protein structures from side‐chain center‐based low‐resolution models is introduced and applied to a set of test proteins with high‐resolution X‐ray structures. The accuracy of the rebuilt all‐atom models is measured by root mean square deviations to the corresponding X‐ray structures and percentages of correct χ1 and χ2 side‐chain dihedrals. The benefit of including Cα positions in the low‐resolution model is examined, and the effect of lattice‐based models on the reconstruction accuracy is discussed. Programs and scripts implementing the reconstruction procedure are made available through the NIH research resource for Multiscale Modeling Tools in Structural Biology (http://mmtsb.scripps.edu). Proteins 2000;41:86–97. © 2000 Wiley‐Liss, Inc.

An improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe-template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. PROSPECTOR also provides predicted contacts and secondary structure for the template-aligned regions, and possibly for the unaligned regions by garnering additional information from other top-scoring threaded structures. Since the lowest-energy structure generated by the simulations is not necessarily the best structure, we employed two structure-selection protocols: distance geometry and clustering. In general, clustering is found to generate somewhat better quality structures in 38 of 68 cases. When applied to the Fischer database, the protocol does no harm and in a significant number of cases improves upon the initial threading model, sometimes dramatically. The procedure is readily automated and can be implemented on a genomic scale.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.