@article {Ortiz1999, title = {Ab initio folding of proteins using restraints derived from evolutionary information}, journal = {Proteins}, volume = {Suppl. 3}, number = {May}, year = {1999}, month = {jan}, pages = {177{\textendash}185}, abstract = {We present our predictions in the ab initio structure prediction category of CASP3. Eleven targets were folded, using a method based on a Monte Carlo search driven by secondary and tertiary restraints derived from multiple sequence alignments. Our results can be qualitatively summarized as follows: The global fold can be considered "correct" for targets 65 and 74, "almost correct" for targets 64, 75, and 77, "half-correct" for target 79, and "wrong" for targets 52, 56, 59, and 63. Target 72 has not yet been solved experimentally. On average, for small helical and alpha/beta proteins (on the order of 110 residues or smaller), the method predicted low resolution structures with a reasonably good prediction of the global topology. Most encouraging is that in some situations, such as with target 75 and, particularly, target 77, the method can predict a substantial portion of a rare or even a novel fold. However, the current method still fails on some beta proteins, proteins over the 110-residue threshold, and sequences in which only a poor multiple sequence alignment can be built. On the other hand, for small proteins, the method gives results of quality at least similar to that of threading, with the advantage of not being restricted to known folds in the protein database. Overall, these results indicate that some progress has been made on the ab initio protein folding problem. Detailed information about our results can be obtained by connecting to http:/(/)www.bioinformatics.danforthcenter.org/+ ++CASP3.}, keywords = {Algorithms, Amino Acid Sequence, Evolution, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Protein Folding, Proteins, Proteins: chemistry}, issn = {0887-3585}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10526366}, author = {Angel. R. Ortiz and Andrzej Koli{\'n}ski and Piotr Rotkiewicz and Bartosz Ilkowski and Jeffrey Skolnick} } @article {Kolinski1999, title = {Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques}, journal = {Biophysical Journal}, volume = {77}, number = {6}, year = {1999}, month = {dec}, pages = {2942{\textendash}52}, abstract = {Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based on the Metropolis sampling scheme, and Entropy Sampling Monte Carlo (ESMC), were applied in a study of a high-resolution lattice model of the C-terminal fragment of the B1 domain of protein G. The results provide a detailed description of folding dynamics and thermodynamics and agree with recent experimental findings (. Nature. 390:196-197). In particular, it was found that the folding is cooperative and has features of an all-or-none transition. Hairpin assembly is usually initiated by turn formation; however, hydrophobic collapse, followed by the system rearrangement, was also observed. The denatured state exhibits a substantial amount of fluctuating helical conformations, despite the strong beta-type secondary structure propensities encoded in the sequence.}, keywords = {Amino Acid Sequence, Animals, Biophysical Phenomena, Biophysics, Models, Molecular, Molecular Sequence Data, Monte Carlo Method, Nerve Tissue Proteins, Nerve Tissue Proteins: chemistry, Protein Conformation, Protein Folding, Protein Structure, Proteins, Proteins: chemistry, Secondary, Thermodynamics}, issn = {0006-3495}, doi = {10.1016/S0006-3495(99)77127-4}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300567\&tool=pmcentrez\&rendertype=abstract}, author = {Andrzej Koli{\'n}ski and Bartosz Ilkowski and Jeffrey Skolnick} } @article {Kolinski1999a, title = {A method for the improvement of threading-based protein models}, journal = {Proteins}, volume = {37}, number = {4}, year = {1999}, month = {dec}, pages = {592{\textendash}610}, abstract = {A new method for the homology-based modeling of protein three-dimensional structures is proposed and evaluated. The alignment of a query sequence to a structural template produced by threading algorithms usually produces low-resolution molecular models. The proposed method attempts to improve these models. In the first stage, a high-coordination lattice approximation of the query protein fold is built by suitable tracking of the incomplete alignment of the structural template and connection of the alignment gaps. These initial lattice folds are very similar to the structures resulting from standard molecular modeling protocols. Then, a Monte Carlo simulated annealing procedure is used to refine the initial structure. The process is controlled by the model{\textquoteright}s internal force field and a set of loosely defined restraints that keep the lattice chain in the vicinity of the template conformation. The internal force field consists of several knowledge-based statistical potentials that are enhanced by a proper analysis of multiple sequence alignments. The template restraints are implemented such that the model chain can slide along the template structure or even ignore a substantial fraction of the initial alignment. The resulting lattice models are, in most cases, closer (sometimes much closer) to the target structure than the initial threading-based models. All atom models could easily be built from the lattice chains. The method is illustrated on 12 examples of target/template pairs whose initial threading alignments are of varying quality. Possible applications of the proposed method for use in protein function annotation are briefly discussed.}, keywords = {Amino Acid Sequence, Computer Simulation, Evaluation Studies as Topic, Methods, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Proteins, Proteins: chemistry, Secondary, Sequence Alignment, Software Design}, issn = {0887-3585}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10651275}, author = {Andrzej Koli{\'n}ski and Piotr Rotkiewicz and Bartosz Ilkowski and Jeffrey Skolnick} }