1/12
Bi1051: Loschmidt Laboratories
Stanislav Mazurenko, PhD
11/05/2020
2/12
Motivation
Experiments
Data
analysis
Analysis for Protein Denaturation
3/12
Input
-1.5
-1
-0.5
0
0.5
1
1.5
2
2.5
40 50 60 70 80
NormilizedSignal
Temperature (oC)
CD & DSF
2.5
3
3.5
4
4.5
5
5.5
6
0 5 10 15 20
Signal
Time (s)
T-jumps
64
66
68
7072
4/12
Data analysis
 Graphs
 Dynamical systems
 Optimization
 















,1
,
,
,
2
211
11
DIN
I
D
IN
I
IN
N
xxx
xk
dt
dx
xkkxk
dt
dx
xkxk
dt
dx
5/12
Results
6/12
-1.5
-1
-0.5
0
0.5
1
1.5
2
2.5
40 50 60 70 80
NormilizedSignal
Temperature (oC)
CD & DSF
Analysis for Microfluidics
7/12
8/12
Microfluidics
Machine Learning for Protein Engineering
9/12
10/12
Artificial Intelligence
towardsdatascience.com
cybercontrols.org
Protein 1: LTLEEIIGIGGFGKV… stable
Protein 2: WIGDEVAVKAARH... unstable
Protein 3: IENVRIGIKLFAML... stable
...
KLAAPPSIGIEPFM… stable
11/12
Predicting protein stability
Protein 1: LTLEEIIGIGGFGKV… stable
Protein 2: WIGDEVAVKAARH... unstable
Protein 3: IENVRIGIKLFAML... stable
...
KLAAPPSIGIEPFM… ?
Ding X, Zou Z, Brooks CL. Deciphering protein evolution and fitness landscapes with latent
space models. Nature Communications. 2019 Dec 10;10(1):1-3.
Further reading
12/12
• Articles:
Musil M, Konegger H, Hon J, Bednar D, Damborsky J. Computational design of stable and
soluble biocatalysts. ACS Catalysis. 2018
Mazurenko S, Prokop Z, Damborský J. Machine Learning in Enzyme Engineering. ACS
Catalysis. 2019
Mazurenko S, Stourac J, Kunka A, Nedeljković S, Bednar D, Prokop Z, Damborsky J. CalFitter:
a web server for analysis of protein thermal denaturation data. Nucleic acids research. 2018
• Courses:
Bi9410 Structural Biology
Bi7430 Molecular biotechnology
Bi9680en Artificial Intelligence in Biology, Chemistry, and Bioengineering