Jianpeng Ma

发表

OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods

Jianpeng Ma, Gang Xu, Qinghua Wang, 2020, J. Chem. Inf. Model..

Improving low-accuracy protein structures using enhanced sampling techniques.

Jianpeng Ma, Qinghua Wang, Tianwu Zang, 2018, The Journal of chemical physics.

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.

Jianpeng Ma, Jianpeng Ma, 2005, Structure.

A New Method for Coarse-Grained Elastic Normal-Mode Analysis.

Jianpeng Ma, Mingyang Lu, Billy Poon, 2006, Journal of chemical theory and computation.

Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble‐based model

Jianpeng Ma, Qinghua Wang, Tianwu Zang, 2018, Protein science : a publication of the Protein Society.

OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks

Jianpeng Ma, Gang Xu, Qinghua Wang, 2020, Bioinform..

OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding

Jianpeng Ma, Gang Xu, Qinghua Wang, 2021, Bioinform..

Conformational transition of amyloid beta-peptide.

Jianpeng Ma, Weiliang Zhu, Hualiang Jiang, 2005, Proceedings of the National Academy of Sciences of the United States of America.

The role of shape in determining molecular motions.

Jianpeng Ma, Mingyang Lu, Jianpeng Ma, 2005, Biophysical journal.

Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill

Jianpeng Ma, Jeffrey K. Noel, José N. Onuchic, 2018, Proceedings of the National Academy of Sciences.

Simulation via direct computation of partition functions.

Jianpeng Ma, Cheng Zhang, 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2002, Structure.

Explicit orientation dependence in empirical potentials and its significance to side-chain modeling.

Jianpeng Ma, Jianpeng Ma, 2009, Accounts of chemical research.

Protein structural transitions and their functional role

Jianpeng Ma, Wei Yang, Martin Karplus, 2005, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

Jing Chen, Jianpeng Ma, Hualiang Jiang, 2013, Proceedings of the National Academy of Sciences.

OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

Jianpeng Ma, Mingyang Lu, Jianpeng Ma, 2008, Journal of molecular biology.

Inhibitor discovery targeting the intermediate structure of beta-amyloid peptide on the conformational transition pathway: implications in the aggregation mechanism of beta-amyloid peptide.

Jianpeng Ma, Xu Shen, Kaixian Chen, 2006, Biochemistry.

OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling.

Jianpeng Ma, Gang Xu, Qinghua Wang, 2020, Journal of chemical theory and computation.

Helical ice-sheets inside carbon nanotubes in the physiological condition

Jianpeng Ma, Richard E. Smalley, Kevin D. Ausman, 2002 .

Counting solutions for the N -queens and Latin-square problems by Monte Carlo simulations.

Jianpeng Ma, Cheng Zhang, 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

Domain movements in human fatty acid synthase by quantized elastic deformational model

Jianpeng Ma, Dengming Ming, S. Wakil, 2002, Proceedings of the National Academy of Sciences of the United States of America.

OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural models

Jianpeng Ma, Tianwu Zang, Tianqi Ma, 2017, bioRxiv.

Why are oseltamivir and zanamivir effective against the newly emerged influenza A virus (A/H1N1)?

Cheng Luo, Jianpeng Ma, Weiliang Zhu, 2009, Cell Research.

Folding helical proteins in explicit solvent using dihedral-biased tempering

Jianpeng Ma, Cheng Zhang, Jianpeng Ma, 2012, Proceedings of the National Academy of Sciences.

Simulation of F-actin filaments of several microns.

Jianpeng Ma, Yinghao Wu, Dengming Ming, 2003, Biophysical journal.

Parallel continuous simulated tempering and its applications in large-scale molecular simulations.

Jianpeng Ma, Tianwu Zang, Jianpeng Ma, 2014, The Journal of chemical physics.

Substructure synthesis method for simulating large molecular complexes

Jianpeng Ma, Yinghao Wu, Dengming Ming, 2002, Proceedings of the National Academy of Sciences of the United States of America.

The unfolding action of GroEL on a protein substrate.

Jianpeng Ma, Martin Karplus, M. Karplus, 2004, Biophysical journal.

Crystal Structure of Unliganded Influenza B Virus Hemagglutinin

Jianpeng Ma, Mingyang Lu, Qinghua Wang, 2008, Journal of Virology.

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase.

Jianpeng Ma, Martin Karplus, Qiang Cui, 2004, Journal of molecular biology.

Theoretical analysis of twist/bend ratio and mechanical moduli of bacterial flagellar hook and filament.

Jianpeng Ma, Jianpeng Ma, Terence C Flynn, 2004, Biophysical journal.

OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.

Jianpeng Ma, Yinghao Wu, Jianpeng Ma, 2009, Journal of molecular biology.

Erratum: Simulated annealing using the classical density distribution [J. Chem. Phys. 101, 533 (1994)]

Jianpeng Ma, John E. Straub, J. Straub, 1995 .

Molecular docking study of the interactions between the thioesterase domain of human fatty acid synthase and its ligands

Jianpeng Ma, Qinghua Wang, F. Quiocho, 2008, Proteins.

Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-Å crystallographic resolution

Jianpeng Ma, Billy K Poon, Xiaorui Chen, 2007, Proceedings of the National Academy of Sciences.

Diversifying selective pressure on influenza B virus hemagglutinin

Jianpeng Ma, Jun Shen, Jianpeng Ma, 2009, Journal of medical virology.

Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation

Jianpeng Ma, John E. Straub, Patricia Amara, 1995 .

Folding of small helical proteins assisted by small-angle X-ray scattering profiles.

Jianpeng Ma, Yinghao Wu, Mingyang Lu, 2005, Structure.

Serine 88 Phosphorylation of the 8-kDa Dynein Light Chain 1 Is a Molecular Switch for Its Dimerization Status and Functions*

Jianpeng Ma, Jianpeng Ma, Mingjie Zhang, 2008, Journal of Biological Chemistry.

Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.

Jianpeng Ma, Eshel Ben-Jacob, Mingyang Lu, 2017, Cancer research.

Conformational transition of amyloid β-peptide

Jianpeng Ma, Weiliang Zhu, Hualiang Jiang, 2005 .

Conformational flexibility of pyruvate dehydrogenase complexes: a computational analysis by quantized elastic deformational model.

Jianpeng Ma, Yinghao Wu, Dengming Ming, 2003, Journal of molecular biology.

Intrinsic flexibility and gating mechanism of the potassium channel KcsA

Jianpeng Ma, Yufeng Shen, Yufeng Shen, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Simulated annealing using the classical density distribution

Jianpeng Ma, John E. Straub, J. Straub, 1994 .

OPUS-Ca: a knowledge-based potential function requiring only Calpha positions.

Jianpeng Ma, Yinghao Wu, Mingyang Lu, 2007, Protein science : a publication of the Protein Society.

Determining protein topology from skeletons of secondary structures.

Jianpeng Ma, Yinghao Wu, Mingyang Lu, 2005, Journal of molecular biology.

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

Jianpeng Ma, Weitao Sun, Tianwu Zang, 2017, Journal of molecular biology.

The crystal structure of murine p97/VCP at 3.6A.

Jianpeng Ma, Hisao Kondo, Paul S Freemont, 2003, Journal of structural biology.

Molecular dynamics analysis of a buckyball–antibody complex

Jianpeng Ma, Jianpeng Ma, Y. Kong, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Motions and negative cooperativity between p97 domains revealed by cryo-electron microscopy and quantised elastic deformational model.

Jianpeng Ma, Hisao Kondo, Paul S Freemont, 2003, Journal of molecular biology.

Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit

Jianpeng Ma, Billy K. Poon, Qinghua Wang, 2009, Acta crystallographica. Section D, Biological crystallography.

OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions

Jianpeng Ma, Yinghao Wu, Mingyang Lu, 2007, Protein science : a publication of the Protein Society.