Sotabase

Career

· Assistant Teaching Professor, University of California, Berkeley2022–
· Lecturer, Stanford University
· MS, Electrical Engineering, Stanford University
· PhD Candidate, Electrical Engineering, Stanford University
· BS, Electrical Engineering and Computer Science, University of California, Berkeley

Publications (41)

A fast and accurate computational approach to protein ionization
Protein Science · 2008
137
cited
LOOPER: a molecular mechanics-based algorithm for protein loop prediction.
Protein engineering, design & selection : PEDS · 2008
124
cited
Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method
Journal of Chemical Information and Modeling · 2008
120
cited
Fully automated antibody structure prediction using BIOVIA tools: Validation study
PLoS ONE · 2017
114
cited
The dominant role of side‐chain backbone interactions in structural realization of amino acid code. ChiRotor: A side‐chain prediction algorithm based on side‐chain backbone interactions
Protein Science · 2007
106
cited
Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds
Journal of Computational Chemistry · 2001
83
cited
pH-selective mutagenesis of protein–protein interfaces: In silico design of therapeutic antibodies with prolonged half-life
Proteins: Structure, Function, and Bioinformatics · 2012
76
cited
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems
Journal of Computational Chemistry · 2003
69
cited
High Speed Networks Need Proactive Congestion Control
ACM Workshop on Hot Topics in Networks · 2015
64
cited
Learning Networking by Reproducing Research Results
CCRV · 2017
59
cited
Fully Automated Molecular Mechanics Based Induced Fit Protein—Ligand Docking Method.
2009
53
cited
TMOSS: Using Intermediate Assignment Work to Understand Excessive Collaboration in Large Classes
Technical Symposium on Computer Science Education · 2018
39
cited
Pensieve: Feedback on Coding Process for Novices
Technical Symposium on Computer Science Education · 2019
34
cited
Molecular basis for the Cu2+ binding-induced destabilization of beta2-microglobulin revealed by molecular dynamics simulation.
Biophysical Journal · 2006
29
cited
Glutamate-115 renders specificity of human 11β-hydroxysteroid dehydrogenase type 2 for the cofactor NAD+
Molecular and Cellular Endocrinology · 2003
26
cited
Unique Exams: Designing Assessments for Integrity and Fairness
Technical Symposium on Computer Science Education · 2020
25
cited
Assessment of putative protein targets derived from the SARS genome
FEBS Letters · 2003
23
cited
A pH‐dependent computational approach to the effect of mutations on protein stability
Journal of Computational Chemistry · 2016
22
cited
Functional annotation of proteomic sequences based on consensus of sequence and structural analysis
Briefings Bioinform. · 2002
22
cited
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
Comput. Biol. Chem. · 2004
14
cited
Sotabase
Lisa Yan | Researcher Profile | Sotabase | Sotabase