- Possible Mechanism for Cold Denaturation of Proteins at High Pressure Manuel I. Marques,1,* Jose M. Borreguero,1
- Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic
- Percolation Theory PR King1, SV Buldyrev2, NV Dokholyan2,4, S Havlin5, E Lopez2, G Paul2,
- Physica A 314 (2002) 103108 www.elsevier.com/locate/physa
- Traveling time and traveling length in critical percolation clusters Youngki Lee,1
- Physica A 266 (1999) 107114 Predicting oil recovery using percolation
- Physica A 274 (1999) 6066 www.elsevier.com/locate/physa
- Physica A 273 (1999) 1932 www.elsevier.com/locate/physa
- Molecular Dynamics Simulation of Amyloid b Dimer Formation B. Urbanc,* L. Cruz,* F. Ding,*y
- Discrete molecular dynamics simulations of peptide aggregation B. Urbanc,1
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- proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Thermodynamics of calmodulin binding to
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- Interaction with the 5D3 Monoclonal Antibody Is Regulated by Intramolecular Rearrangements but Not by Covalent
- Multiple Folding Pathways of the SH3 Domain Jose M. Borreguero,* Feng Ding,y
- COMMUNICATION Functional Fingerprints of Folds: Evidence for
- Insights into thermophilic archaebacterial membrane stability from simplified models of lipid membranes
- Can Contact Potentials Reliably Predict Stability of Proteins?
- Scale-Free Evolution: From Proteins to Organisms
- Deciphering Protein Dynamics from NMR Data Using Explicit Structure Sampling and Selection
- Journal of Statistical Physics, Vol. 93, Nos. 3/4, 1998 Scaling of the Distribution of Shortest Paths
- MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Shuangye Yin,
- Measurement of magnetic moments of free BiNMnM clusters Shuangye Yin, Xiaoshan Xu, Ramiro Moro,* and Walt A. de Heer
- A Single Disulfide Bond Differentiates Aggregation Pathways of 2-Microglobulin
- The rate and equilibrium constants for a multistep reaction sequence for the aggregation of superoxide
- Using protein design for homology detection and active site searches
- MultiscaleQ1 approaches for studying energy transduction in dynein Adrian W. R. Serohijos,*acd
- Subscriber access provided by UNIV OF NORTH CAROLINA Journal of the American Chemical Society is published by the American Chemical
- COMMUNICATION Identifying the Protein Folding Nucleus Using
- Combining Fluorescence Detection and Mass Spectrometric Analysis for Comprehensive and
- Author's personal copy Protein folding: Then and now
- Spin Uncoupling in Free Nb Clusters: Support for Nascent Superconductivity Ramiro Moro, Shuangye Yin, Xiaoshan Xu, and Walt A. de Heer
- Modeling Backbone Flexibility Improves Protein Stability Estimation
- Predicting Oil Recovery using Percolation Theory , SV Buldyrev2
- eQTL Analysis by Linear Model November 19, 2009
- Protein folding: Then and now Yiwen Chen 1
- Supplemental Data: The path of DNA in the kinetochore Kerry Bloom, Shantanu Sharma, and Nikolay Dohkolyan
- UNCORRECTED 3 Protein folding: Then and now
- Studies of folding and misfolding using simplified models Nikolay V Dokholyan
- John von Neumann Institute for Computing Simplified Approaches to Complex
- G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase*S Received for publication,December 2, 2008, and in revised form, January 15, 2009 Published, JBC Papers in Press,January 27, 2009, DOI 10.1074/jbc.M809058200
- Khare and Dokholyan. 10.1073/pnas.0511266103 Supporting Information
- SHORT COMMUNICATION What Is the Protein Design Alphabet?
- Physica A 314 (2002) 600606 www.elsevier.com/locate/physa
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- Meeting Review Outcome of a Workshop on Applications
- Kinetic models for the coordinated stepping of cytoplasmic dynein Denis Tsygankov,1,a
- BiPS, a Photocleavable, Isotopically Coded, Fluorescent Cross-linker for Structural
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- BIOINFORMATICS APPLICATIONS NOTE Vol. 24 no. 17 2008, pages 19511952
- Natural Selection against Protein Aggregation on Self-Interacting and Essential Proteins in Yeast, Fly, and Worm
- Computational Studies Reveal Phosphorylation-dependent Changes in the
- 10.1261/rna.894608Access the most recent version at doi: 2008 14: 1164-1173; originally published online May 2, 2008;RNA
- Diminished Self-Chaperoning Activity of the DF508 Mutant of CFTR Results in Protein Misfolding
- [Frontiers in Bioscience 4795-4808, May 1, 2008] Probing protein aggregation using discrete molecular dynamics
- New and Notable DNA Sequence Mediates
- This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and
- This article was published in an Elsevier journal. The attached copy is furnished to the author for non-commercial research and
- The Length Dependence of the PolyQ-mediated Protein Aggregation*
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- FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale
- 12 Katz, L. and Burge, C.B. (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res.
- Supplementary material The coordinated evolution of
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- ISSN 1553-734X Published in association with the International Society for Computational Biology
- Supporting Text Dot Blotting
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- Imaging single living cells with a scanning near-eld infrared microscope based on a free electron laser
- Physica A 249 (1998) 594599 Model of unequal chromosomal crossing over
- 22 September 1994 PHYSICS LETTERS B
- Structure 14, 514, January 2006 2006 Elsevier Ltd All rights reserved DOI 10.1016/j.str.2005.09.008 Topological Determinants of
- Fast screening of protein surfaces using geometric invariant fingerprints
- Yin et al. MedusaScore: An Accurate Force-Field Based Scoring Function for Virtual Drug Screening Table S1. List of atom types and parameters of MedusaScore.
- 466 | VOL.4 NO.6 | JUNE 2007 | NATURE METHODS CORRESPONDENCE
- Magnetic Enhancement in Cobalt-Manganese Alloy Clusters Shuangye Yin, Ramiro Moro, Xiaoshan Xu, and Walter A. de Heer
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- Sharma, Ding, & Dokholyan, "Multiscale modeling of nucleosome dynamics" SUPPLEMENTAL DATA
- Supporting Information Ding and Dokholyan 10.1073/pnas.0803266105
- This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at http://www.biophysj.org. The final
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- [25] Identifying Importance of Amino Acids for Protein Folding from Crystal Structures
- Towards Unifying Protein Evolution Theory N.V. Dokholyan and E.I. Shakhnovich
- Physica A 249 (1998) 430438 Analysis of DNA sequences using methods
- Physica A 266 (1999) 5561 Distribution of shortest paths in percolation
- ? Author to whom correspondence should be addressed. E-mail: dokh@wild.harvard.edu
- Supplementary Material Hao et al. Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel
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- 2962 Biophysical Journal Volume 85 November 2003 29622972 Protein Evolution within a Structural Space
- Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion*
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- Supplementary Materials Geometry of the Protein Model: To model hydrogen bonding more accurately, we add the
- Ding F, Dokholyan NV (2006) Emergence of protein fold families through rational design. PLoS Comput Biol 2(7): e85. DOI: 10.1371/journal.pcbi.0020085
- Published in association with the International Society for Computational Biology PUBLIC LIBRARY of SCIENCE | ploscompbiol.org | Volume 2 | Issue 7 | JULY 2006
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- This Article Email this article to a colleague
- Structure, Vol. 13, 10471054, July, 2005, 2005 Elsevier Ltd All rights reserved. DOI 10.1016/j.str.2005.04.009 Scaling Behavior and Structure
- Journal of Alzheimer's Disease 6 (2004) 99105 99 Live discussion: Protein folding and
- proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS N-terminal strands of filamin Ig domains
- Supporting Information Yin et al. 10.1073/pnas.0906146106
- DOI: 10.1126/science.1083247 , 1265 (2003);300Science
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- A. Bonetti et al. (eds.), Platinum and Other Heavy Metal Compounds 157 Humana Press, a part of Springer Science + Business Media, LLC 2009
- VOLUME 86, NUMBER 10 P H Y S I C A L R E V I E W L E T T E R S 5 MARCH 2001 Novel Structures and Properties of Gold Nanowires
- J Supercond Nov Magn (2008) 21: 265269 DOI 10.1007/s10948-008-0332-1
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- Structure, Vol. 12, 21612171, December, 2004, 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.str.2004.09.011 New Insights into FAK Signaling
- Phenylalanine-508 mediates a cytoplasmicmembrane domain contact in the CFTR 3D structure crucial
- Supporting Text Sequence Threading
- Vol. 22 no. 21 2006, pages 26932694 doi:10.1093/bioinformatics/btl460BIOINFORMATICS APPLICATIONS NOTE
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- Supplementary Text S1. KD was calculated for binding of HMGB1a to CP-and OX-DNA in the TGGA, AGGC and CGGA
