Feng Ding
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Feng Dingcomputer-science Degrees
Computer Science
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Machine Learning
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Artificial Intelligence
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Computer Science
Feng Ding's Degrees
- PhD Computer Science University of California, Berkeley
- Masters Computer Science University of California, Berkeley
- Bachelors Computer Science Tsinghua University
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Why Is Feng Ding Influential?
(Suggest an Edit or Addition)Feng Ding's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Automated minimization of steric clashes in protein structures (2011) (569)
- Eris: an automated estimator of protein stability (2007) (354)
- Ab initio folding of proteins with all-atom discrete molecular dynamics. (2008) (282)
- Topological determinants of protein folding (2002) (276)
- Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. (2008) (273)
- RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012) (235)
- iFoldRNA: three-dimensional RNA structure prediction and folding (2008) (201)
- Mechanism for the α‐helix to β‐hairpin transition (2003) (189)
- Molecular Dynamics Simulation of Amyloid β Dimer Formation (2004) (178)
- Engineered allosteric activation of kinases in living cells (2010) (177)
- Emergence of Protein Fold Families through Rational Design (2006) (169)
- RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015) (165)
- Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. (2012) (165)
- Modeling backbone flexibility improves protein stability estimation. (2007) (160)
- RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. (2017) (158)
- Molecular dynamics simulation of the SH3 domain aggregation suggests a generic amyloidogenesis mechanism. (2002) (157)
- Dynamical roles of metal ions and the disulfide bond in Cu, Zn superoxide dismutase folding and aggregation (2008) (142)
- Direct molecular dynamics observation of protein folding transition state ensemble. (2002) (121)
- Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. (2004) (119)
- Rational design of a ligand-controlled protein conformational switch (2013) (105)
- Multiscale modeling of nucleosome dynamics. (2007) (103)
- Molecular Origin of Polyglutamine Aggregation in Neurodegenerative Diseases (2005) (102)
- On the significance of an RNA tertiary structure prediction. (2010) (100)
- Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences (2010) (98)
- Discrete molecular dynamics (2012) (95)
- Protein folding: then and now. (2008) (92)
- Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands (2010) (86)
- Structural and dynamic determinants of protein-peptide recognition. (2011) (81)
- Discrete molecular dynamics simulations of peptide aggregation. (2003) (81)
- Simple but predictive protein models. (2005) (80)
- Fast complementation of split fluorescent protein triggered by DNA hybridization (2006) (79)
- Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion* (2005) (79)
- Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. (2009) (77)
- Three-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing (2012) (75)
- Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. (2005) (74)
- Topological determinants of protein domain swapping. (2006) (73)
- Local unfolding of Cu, Zn superoxide dismutase monomer determines the morphology of fibrillar aggregates. (2012) (71)
- New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. (2004) (69)
- Correction: Emergence of Protein Fold Families through Rational Design (2006) (63)
- Harnessing a Physiologic Mechanism for siRNA Delivery With Mimetic Lipoprotein Particles (2012) (62)
- Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. (2003) (60)
- Scaling behavior and structure of denatured proteins. (2005) (59)
- RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers (2020) (58)
- Structural and thermodynamic effects of post-translational modifications in mutant and wild type Cu, Zn superoxide dismutase. (2011) (51)
- Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions (2008) (49)
- Molecular dynamics simulation of amyloid beta dimer formation. (2004) (47)
- Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark (2013) (45)
- Gaia: automated quality assessment of protein structure models (2011) (45)
- Multiple folding pathways of the SH3 domain. (2003) (40)
- The Length Dependence of the PolyQ-mediated Protein Aggregation* (2007) (39)
- Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. (2010) (37)
- Computational approaches to understanding protein aggregation in neurodegeneration. (2014) (35)
- Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics. (2013) (34)
- A structural model reveals energy transduction in dynein (2006) (34)
- Parallel folding pathways in the SH3 domain protein. (2007) (34)
- G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase* (2009) (33)
- iFold: a platform for interactive folding simulations of proteins (2006) (31)
- Hybrid dynamics simulation engine for metalloproteins. (2012) (28)
- Fidelity of the protein structure reconstruction from inter-residue proximity constraints. (2007) (27)
- Molecular Dynamics Simulation of Amyloid b Dimer Formation (2004) (27)
- Chemical and Biophysical Signatures of the Protein Corona in Nanomedicine. (2022) (26)
- Identifying importance of amino acids for protein folding from crystal structures. (2003) (25)
- Structural basis for μ-opioid receptor binding and activation. (2011) (25)
- Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches (2013) (22)
- Probing protein aggregation using discrete molecular dynamics. (2008) (21)
- N‐terminal strands of filamin Ig domains act as a conformational switch under biological forces (2010) (20)
- New models of Tetrahymena telomerase RNA from experimentally derived constraints and modeling. (2012) (18)
- Structure modeling of RNA using sparse NMR constraints (2017) (17)
- Statistical analysis of SHAPE-directed RNA secondary structure modeling. (2013) (15)
- Discrete Molecular Dynamics Simulation of Biomolecules (2012) (15)
- RNA tertiary structure analysis by 2'-hydroxyl molecular interference. (2014) (15)
- Probing interdomain linkers and protein supertertiary structure in vitro and in live cells with fluorescent protein resonance energy transfer. (2020) (14)
- Computational evaluation of protein stability change upon mutations. (2010) (9)
- Multiscale Modeling of RNA Structure and Dynamics (2012) (6)
- DMD: An Efficient And Versatile Simulation Method For Fine Protein Characterization (2012) (6)
- Posttranslational Modifications Promote Formation of SOD1 Oligomers With Potential Toxicity in ALS (2014) (3)
- Hydrophobic/Hydrophilic Ratio of Amphiphilic Helix Mimetics Determines the Effects on Islet Amyloid Polypeptide Aggregation (2022) (3)
- A hidden aggregation‐prone structure in the heart of hypoxia inducible factor prolyl hydroxylase (2016) (2)
- Correction to Robust and Generic RNA Modeling Using Inferred Constraints: A Structure for the Hepatitis C Virus IRES Pseudoknot Domain (2010) (2)
- Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics (2010) (2)
- Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions (2021) (1)
- Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models (2022) (1)
- Substoichiometric Inhibition of Insulin against IAPP Aggregation Is Attenuated by the Incompletely Processed N-Terminus of proIAPP. (2022) (1)
- SAMase of Bacteriophage T3 Inactivates Escherichia coli’s Methionine S-Adenosyltransferase by Forming Heteropolymers (2021) (1)
- Ju n 20 03 1 Folding of Cu , Zn superoxide dismutase and Familial Amyotrophic Lateral Sclerosis (2008) (0)
- Computational Modeling of Telomerase in Action (2012) (0)
- An 86 amino acids motif in CAPN3 is essential for formation of the nucleolus-localized Def-CAPN3 complex. (2022) (0)
- Chapter 9 Multiscale Modeling of RNA Structure and Dynamics (2012) (0)
- structure prediction : A CASP-like evaluation of RNA three-dimensional RNA-Puzzles (2012) (0)
- Faculty Opinions recommendation of Critical nucleus size for disease-related polyglutamine aggregation is repeat-length dependent. (2011) (0)
- Inter-domain linkers modulate supertertiary structural dynamics in the N-terminal PDZ tandem of PSD-95 (2022) (0)
- Multiscalar nucleosome dynamics in silico ‐ Role of DNA and histone tails (2007) (0)
- Effect of Bio-molecules on Human Islet Amyloid Polypeptide Aggregation, Fibril Remodeling and Cytoxicity (2018) (0)
- Faculty Opinions recommendation of Single-molecule derivation of salt dependent base-pair free energies in DNA. (2010) (0)
- Understanding the Endogenous Inhibition of IAPP Aggregation (2018) (0)
- Computational approachestounderstandingprotein aggregation in neurodegeneration (2014) (0)
- Model for the Dynein Motor Unit (2006) (0)
- SAMase of bacteriophage T3 inactivates Escherichia coli's methionine sadenosyltransferase by forming hetero-polymers (2021) (0)
- MAT in complex with SAMH (2021) (0)
- RNA Three-Dimensional Structure Determination Using Experimental Constraints (2013) (0)
- Computational study of nanoparticle-induced endothelial leakiness (2022) (0)
- SAMase of bacteriophage T3 inactivates E. coli’s methionine S-adenosyltransferase by forming hetero-polymers (2021) (0)
- Different Forms of Disorder in NMDA-Sensitive Glutamate Receptor Cytoplasmic Domains Are Associated with Differences in Condensate Formation (2022) (0)
- Multiscale Modeling of RNA Structure 3 and Dynamics 4 (2012) (0)
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What Schools Are Affiliated With Feng Ding?
Feng Ding is affiliated with the following schools:
