Buyong Ma

发表

Principles of docking: An overview of search algorithms and a guide to scoring functions

Ruth Nussinov, Inbal Halperin, Buyong Ma, 2002, Proteins.

Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example.

Ruth Nussinov, Ruxi Qi, Guanghong Wei, 2018, Methods in molecular biology.

Ligand Binding and Circular Permutation Modify Residue Interaction Network in DHFR

Ruth Nussinov, Zengjian Hu, Yongping Pan, 2007, PLoS Comput. Biol..

Coupling of Zinc-Binding and Secondary Structure in Nonfibrillar Aβ40 Peptide Oligomerization

Yonggang Chen, Liang Xu, Ruth Nussinov, 2015, J. Chem. Inf. Model..

Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

Jenn-Huei Lii, Norman L. Allinger, Buyong Ma, 1999, J. Comput. Chem..

Defining the Domain Arrangement of the Mammalian Target of Rapamycin Complex Component Rictor Protein

Ruth Nussinov, Ping Zhou, Ning Zhang, 2015, J. Comput. Biol..

The origin of Allosteric Modulation: Multiple Pre-existing Pathways Selection

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2009 .

A hierarchical, building-block-based computational scheme for protein structure prediction

Sandeep Kumar, Ruth Nussinov, Haim J. Wolfson, 2001, IBM J. Res. Dev..

Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm

Ruth Nussinov, Amarda Shehu, Rudy Clausen, 2015, PLoS Comput. Biol..

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

Ruth Nussinov, Amarda Shehu, Tatiana Maximova, 2016, PLoS Comput. Biol..

Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics

Ruth Nussinov, Amarda Shehu, Kazi Lutful Kabir, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

A MOLECULAR MECHANICS STUDY OF THE CHOLESTERYL ACETATE CRYSTAL : EVALUATION OF INTERCONVERSION AMONG RG, RZ, AND RA BOND LENGTHS

Jenn-Huei Lii, Norman L. Allinger, Buyong Ma, 1997 .

Conformational Basis for Asymmetric Seeding Barrier in Filaments of Three- and Four-Repeat Tau

Ruth Nussinov, Gareth R. Eaton, Sandra S. Eaton, 2012, Journal of the American Chemical Society.

Metal binding sites in amyloid oligomers: Complexes and mechanisms

Ruth Nussinov, Buyong Ma, R. Nussinov, 2012 .

Molecular dynamics simulations of the unfolding of β2‐microglobulin and its variants

Ruth Nussinov, Buyong Ma, R. Nussinov, 2003 .

Systematic Comparison of Experimental, Quantum Mechanical, and Molecular Mechanical Bond Lengths for Organic Molecules

Jenn-Huei Lii, Norman L. Allinger, Buyong Ma, 1996 .

Regulating highly dynamic unstructured proteins and their coding mRNAs

Ruth Nussinov, Buyong Ma, R. Nussinov, 2009, Genome Biology.

Consensus features in amyloid fibrils: sheet–sheet recognition via a (polar or nonpolar) zipper structure

Ruth Nussinov, Buyong Ma, R. Nussinov, 2006, Physical biology.

Synergistic Interactions between Repeats in Tau Protein and Aβ Amyloids May Be Responsible for Accelerated Aggregation via Polymorphic States

Ruth Nussinov, Buyong Ma, R. Nussinov, 2011, Biochemistry.

Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.

Jie Liang, Ozlem Keskin, Ruth Nussinov, 2004, Journal of molecular biology.

Single mutations in tau modulate the populations of fibril conformers through seed selection.

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2014, Angewandte Chemie.

Conservation of polar residues at protein interfaces.

Buyong Ma, R. Nussinov, Zengjian Hu, 2000 .

Energy landscape and dynamics of the β‐hairpin G peptide and its isomers: Topology and sequences

Ruth Nussinov, Buyong Ma, R. Nussinov, 2003, Protein science : a publication of the Protein Society.

Calculation of rz structures from rs structures

Norman L. Allinger, Buyong Ma, B. Ma, 1997 .

Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets

Ruth Nussinov, Buyong Ma, Arnold J. Levine, 2007, Nucleic acids research.

Why Does Binding of Proteins to DNA or Proteins to Proteins Not Necessarily Spell Function?

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2010, ACS chemical biology.

Selective molecular recognition in amyloid growth and transmission and cross-species barriers.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2012, Journal of molecular biology.

A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single beta-sheet model with a small hydrophobic core.

Ruth Nussinov, Nurit Haspel, David Zanuy, 2005, Journal of molecular biology.

Triggering loops and enzyme function: identification of loops that trigger and modulate movements.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2003, Journal of molecular biology.

Amplification of signaling via cellular allosteric relay and protein disorder

Ruth Nussinov, Buyong Ma, R. Nussinov, 2009, Proceedings of the National Academy of Sciences.

Conformational distribution and α-helix to β-sheet transition of human amylin fragment dimer.

Ruth Nussinov, Ruxi Qi, Guanghong Wei, 2014, Biomacromolecules.

Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer's β by solid-state NMR spectroscopy.

Ruth Nussinov, Buyong Ma, Yoshitaka Ishii, 2011, Journal of the American Chemical Society.

Simulations as analytical tools to understand protein aggregation and predict amyloid conformation.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2006, Current opinion in chemical biology.

Protein dynamics: Conformational footprints.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2016, Nature chemical biology.

Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2018, Methods in molecular biology.

Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states

Ruth Nussinov, Buyong Ma, R. Nussinov, 2010, Proceedings of the National Academy of Sciences.

Principles of Protein—Protein Interactions: What Are the Preferred Ways for Proteins to Interact?

Ozlem Keskin, Ruth Nussinov, Attila Gursoy, 2008 .

Druggable orthosteric and allosteric hot spots to target protein-protein interactions.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2014, Current pharmaceutical design.

Molecular Dynamics Simulations of the Denaturation and Refolding of an RNA Tetraloop

Bruce A. Shapiro, Buyong Ma, Wen Li, 2001, Journal of biomolecular structure & dynamics.

Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning.

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2017, Physical chemistry chemical physics : PCCP.

Folding funnels and conformational transitions via hinge-bending motions

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2007, Cell Biochemistry and Biophysics.

The unique Alzheimer's β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2011, Journal of the American Chemical Society.

Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2003, Protein engineering.

Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2012, The Journal of Biological Chemistry.

Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein.

Ruth Nussinov, Qingwen Zhang, Buyong Ma, 2016, ACS chemical neuroscience.

How do transcription factors select specific binding sites in the genome?

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2009, Nature Structural &Molecular Biology.

Peptide–MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites

Ruth Nussinov, John Orban, Yihong Chen, 2018, The Journal of Biological Chemistry.

Theoretical Studies of the Potential Energy Surfaces and Compositions of the d-Aldo- and d-Ketohexoses

Norman L. Allinger, Henry F. Schaefer, Buyong Ma, 1998 .

Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape toward homo-dimerization.

Ruth Nussinov, Ruxi Qi, Guanghong Wei, 2016, Protein engineering, design & selection : PEDS.

Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

Jenn-Huei Lii, Norman L. Allinger, Buyong Ma, 1999 .

Hollow core of Alzheimer’s Aβ42 amyloid observed by cryoEM is relevant at physiological pH

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2010, Proceedings of the National Academy of Sciences.

Cooperativity among Short Amyloid Stretches in Long Amyloidogenic Sequences

Yu-Dong Cai, Buyong Ma, B. Ma, 2012, PloS one.

Structural disorder in four-repeat Tau fibrils reveals a new mechanism for barriers to cross-seeding of Tau isoforms

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2018, The Journal of Biological Chemistry.

Dipeptide analysis of p53 mutations and evolution of p53 family proteins.

Ruth Nussinov, Arnold J Levine, Buyong Ma, 2014, Biochimica et biophysica acta.

Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2016, Physical chemistry chemical physics : PCCP.

Molecular insights into the reversible formation of tau protein fibrils.

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2013, Chemical communications.

Mechanisms of recognition of amyloid-β (Aβ) monomer, oligomer, and fibril by homologous antibodies

Ruth Nussinov, Buyong Ma, R. Nussinov, 2017, The Journal of Biological Chemistry.

Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2006, Biophysical journal.

Protein dynamics and conformational selection in bidirectional signal transduction

Ruth Nussinov, Buyong Ma, R. Nussinov, 2012, BMC Biology.

In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1.

Ruth Nussinov, Arnold J Levine, Buyong Ma, 2005, Biochemistry.

Aβ(1–42) Fibril Structure Illuminates Self-recognition and Replication of Amyloid in Alzheimer’s

Ruth Nussinov, Buyong Ma, Yoshitaka Ishii, 2015, Nature Structural &Molecular Biology.

Enzyme dynamics point to stepwise conformational selection in catalysis.

Ruth Nussinov, Buyong Ma, R. Nussinov, 2010, Current opinion in chemical biology.

Molecular polarizabilities and induced dipole moments in molecular mechanics

Jenn-Huei Lii, Norman L. Allinger, Buyong Ma, 2000 .

Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer.

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2017, Journal of molecular biology.

A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery.

Ruth Nussinov, Chung-Jung Tsai, Buyong Ma, 2013, Biochimica et biophysica acta.

Alzheimer Aβ Amyloid Annular Fibrils: Insight Into Polymorphism

Ruth Nussinov, Buyong Ma, Yifat Miller, 2011 .

Structural Insight into Tau Protein’s Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation

Ruth Nussinov, Guanghong Wei, Buyong Ma, 2014, The journal of physical chemistry letters.