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Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking. Journal of chemical information and modeling 51, 370-7 (2011).
X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct800239q>
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101-5 (2011).
On the use of low resolution data to improve structure predictions of proteins and protein complexes. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct900305m>
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16208716&query_hl=4&itool=pubmed_docsum>
Unravelling the hidden DNA structural/physical code provides novel insights on promoter location. Nucleic acids research 41, 7220-30 (2013).
United-atom discrete molecular dynamics of proteins using physics-based potentials. (2008).at <http://pubs.acs.org/doi/abs/10.1021/ct8003832>
Unique Tautomeric and Recognition Properties of Thioketothymines?. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ja904880y>
Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations. PLoS computational biology 9, e1003354 (2013).
Unconventional interactions between water and heterocyclic nitrogens in protein structures. (2004).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15326588&query_hl=1&itool=pubmed_DocSum>
Triplex formation using oligonucleotide clamps carrying 8-aminopurines. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/18058521>
Towards a Consensus view of duplex RNA flexibility. (2010).at <http://www.cell.com/biophysj/retrieve/pii/S0006349510008052>
Towards a consensus view of B-DNA flexibility. (2008).at <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367714/>
Toward an atomistic description of the urea-denatured state of proteins. Proceedings of the National Academy of Sciences of the United States of America 110, 5933-8 (2013).
Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17502102>
Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO detoxification mechanism. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15783226&query_hl=1&itool=pubmed_DocSum>
Theoretical study of large conformational transitions in DNA: The B<->A conformational change in water and ethanol/water. (2007).at <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904281/>
Theoretical Characterization of the Dynamical Behavior and Transport Properties of alpha,gamma-Peptide Nanotubes in Solution. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ja903400n>
Theoretical Analysis of Antisense Duplexes: Determinants of the RNase H Susceptibility. (2008).at <http://www.ncbi.nlm.nih.gov/pubmed/18298115>
Target Flexibility: An Emerging Consideration in Drug Discovery and Design. (2008).at <http://pubs.acs.org/doi/abs/10.1021/jm800562d>
A systematic study of the energetics involved in structural changes upon association and connectivity in protein-protein interaction networks. (2011).
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks. Structure (London, England : 1993) 19, 881-9 (2011).
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. (2009).at <http://nar.oxfordjournals.org/content/38/1/299.abstract>
Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. (2008).at <http://pubs.acs.org/doi/abs/10.1021/jo801665k>
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. Journal of chemical theory and computation 9, 707-721 (2013).
Structure of triplex DNA in the gas phase. Journal of the American Chemical Society 134, 6596-606 (2012).
Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization. (2007).at <http://www.jbc.org/content/282/43/31444.abstract>
Structural Properties of G.T-parallel duplexes carrying 8-aminopurine residues. (2009).at <http://www.sage-hindawi.com/journals/jna/2010/763658.html>
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases. The journal of physical chemistry. A 115, 11344-54 (2011).
Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. (2010).at <http://dx.doi.org/10.1016/j.jmb.2010.08.029>
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering. Journal of molecular biology 406, 604-19 (2011).
Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures. The FEBS journal (2013).doi:10.1111/febs.12670
Solvation enthalpies of neutral solutes in water and octanol. (2009).at <http://www.springerlink.com/content/wx2k5l0h850x8n60/>
Small Molecule Docking from Theoretical Structural Models. Computational Modeling of Biological Systems Biological and Medical Physics, Biomedical Engineering 75-95 (2012).
Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. (2009).at <http://pubs.acs.org/doi/abs/10.1021/ct900200k>
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. (2007).at <http://www.ncbi.nlm.nih.gov/pubmed/17351000>
PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for geotyping purporses. (2005).
Proteins in the gas phase. (2013).
The protein folding transition-state ensemble from a Gō-like model. Physical chemistry chemical physics : PCCP 13, 15166-74 (2011).
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials. (2009).at <http://onlinelibrary.wiley.com/doi/10.1002/prot.22563/abstract>
A Procedure for the identification of homologous alternative splicing events. (2007).at <http://www.biomedcentral.com/1471-2105/8/260>
Polarization effects in molecular interactions. (2011).at <http://onlinelibrary.wiley.com/doi/10.1002/wcms.32/abstract>
PMUT: A Web-based tool for the annotation of pathological mutations on proteins. (2005).at <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15879453&query_hl=1&itool=pubmed_DocSum>
Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC genomics 12, 489 (2011).
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies. (2010).at <http://www.springerlink.com/content/t04014112597w443/>
Performance of the IEF-MST Solvation Continuum Model in a Blind Test Prediction of Hydration Free Energies. (2009).at <http://pubs.acs.org/doi/abs/10.1021/jp903514u>
Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA hairpins. (2010).at <http://pubs.acs.org/doi/abs/10.1021/ct100481h>