2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Deep Learning for Assignment of Protein
Secondary Structure Elements from Cα Coordinates
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) | 978-1-6654-0126-5/21/$31.00 ©2021 IEEE | DOI: 10.1109/BIBM52615.2021.9669538
Kamal Al Nasr*
Department of Computer Science Department of Computer Science
Tennessee State University Tennessee State University
Nashville, TN, USA Nashville, TN, USA
kalnasr@tnstate.edu asekmen@tnstate.edu
Christopher Jones
Department of Computer Science
Tennessee State University
Nashville, TN, USA
cjone141@tnstate.edu
Abstract—This paper presents a Deep Neural network (DNN)
system that uses a large set of geometric and categorical features
for classification of secondary structure elements (SSEs) in the
protein’s trace that consists of Cα atoms on the backbone. A
systematical approach is implemented for classification of protein
SSE problem. This approach consists of two network architecture
search (NAS) algorithms for selecting (1) network architecture
and layer connectivity, and (2) regularization parameters. Each
algorithm uses a different search space and they are used in
succession to develop a DNN. The DNN system generates over
93% classification rate on average for multiple test sets without
any post processing for amino acid configurations.
Index Terms—protein modeling, secondary structure classifi-
cation, Cα backbone, deep neural networks
I. I NTRODUCTION
Proteins are molecules made of a sequence of amino acids
(i.e., residues), which perform a crucial role in cells. Each
protein folds into a specific 3 dimensional (i.e., 3D ) spatial
structure and can interact with other molecules [1]–[3]. Deter-
mination of the 3D structure is a key process to interpret its
biological function and has gained a primary concern in bio-
logical research fields and intelligent drug design. Many exper-
imental methods have been used, conventionally, to determine
the structure of a protein including X-Ray crystallography
[4]–[6], Nuclear Magnetic Resonance [7], [8], and Cryogen-
Electron Microscopy [4], [9], [10]. Protein folding is governed
by some chemical forces and forms local sub-conformations
during its folding process. These sub-conformations are called
secondary structure elements (SSEs) and they are stabilized
by hydrogen bonds. The most common types of SSEs are
helices and sheets. Helices are SSEs stabilized by hydrogen-
bonding between N − H group and C = O group of peptide
bonds four residues apart. Sheets are composed of two or more
different segments (i.e., strands) stretch along the structure
Ali Sekmen’s research is supported by DOD grant W911NF-20-100284.
Kamal Al Nasr’s research is supported by NIH Academic Research Enhance-
ment Award (R15 AREA: 1R15GM126509 01).* Corresponding author
978-1-6654-0126-5/21/$31.00 ©2021 IEEE
Authorized licensed use limited to: Trial User - Warsaw University (Uniwersytet Warszawski). Downloaded on April 15,2023 at 22:27:49 UTC from IEEE Xplore. Restrictions apply.
Ali Sekmen Bahadir Bilgin
Department of Mechanical Engineering
Middle East Technical University
Ankara, Turkey
bahadir.bilgin@metu.edu.tr
Ahmet Bugra Koku
Department of Mechanical Engineering
Middle East Technical University
Ankara, Turkey
kbugra@metu.edu.tr
of the protein. Sheets are stabilized by hydrogen-bonding
between N − H group of one strand with C = O group of an
adjacent strand. The rest of amino acids that are not involved
in one of the two main SSEs in protein structure form what is
called loops/coils. Therefore, identifying/assigning these SSEs
is crucial in protein structure determination.
Secondary structure assignments have diverse applications
in protein science and analysis. It is used in structure com-
parison and classification. Further, it is important for protein
modeling and structure prediction. Secondary structures have
also been employed in protein modeling, structure prediction,
protein dynamics, and protein-protein interaction. Many ex-
perimental methods have been conventionally used to assign
SSEs. Optical spectroscopy is a fast technique and has been
used to inspect hydrogen-bond dynamics at a picosecond time
scale for a small b-turn peptide [11]. On the other hand,
circular dichroism (CD) and Raman spectroscopy are used
to characterize overall protein secondary structure dynamics
in solution, since the helix and sheet structures give strong
characteristic spectra which are highly correlated with X-ray
data [12]–[14].
Experimental methods of protein structure determination
have many limitations including crystallization, resolution,
time, and cost. In contrast, protein sequencing (i.e., deter-
mining the sequence of amino acids making up the protein)
is less expensive and faster [15]. Therefore, there is a huge
gap between the number of determined structures and the
number of determined sequences. With the computational
power we have nowadays, several computational techniques
are recently used to model structures of proteins (i.e., find the
spatial arrangements of amino acids) to close the gap. These
techniques include ab initio modeling [16]–[18], comparative
modeling [19], [20], and de novo modeling [21]–[25]. These
modeling techniques generate structural information of a pro-
tein. However, modeling techniques may not necessarily find
the structure of a protein at atomic resolution. Therefore, they
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 may model a portion of a protein, its backbone chain, or a
trace of Cα coordinates.
When a protein structure is determined, it is made available
to research community through some unified databases. One
popular database is Protein Data Bank (PDB) [1], [26]. Each
protein molecule has an entry in PDB with a unique alphanu-
meric ID number. The entry contains information about the
protein including information about SSEs. This information
includes the group of amino acids forming the SSEs and
the type of each SSE. The information about SSEs in PDB
entries are coming from experimental methods. When the
experimental method is not available, several computational
methods can be used when all-atom structure is available.
The most popular computational method is Define Secondary
Structure of Proteins (DSSP) [27], [28]. DSSP is a pattern-
recognition process of hydrogen-bonded and geometrical fea-
tures extracted from X-ray coordinates. DSSP algorithm be-
comes one of the standard methods used to assign secondary
structure annotation to amino acids of proteins when the
complete structure is available. DSSP is based primarily on
hydrogen-bonding patterns and geometrical feature constraints
extracted from protein structure coordinates. DSSP calculates
the intra-backbone hydrogen bonds of the protein between
nitrogen and carbonyl groups along the protein polypeptide
chain using a Coulomb approximation of the hydrogen-bond
energy function [29]. The original version of DSSP (now
called DSSPold) was rewritten in 2012 to improve the accu-
racy of π-helix assignment [30]. Another popular algorithms
that is widely used is called STRIDE [31]. STRIDE aims to
provide secondary structure assignments that are more consis-
tent with experimental assignments. STRIDE uses additional
features such as dihedral angle propensities. STRIDE has been
optimized on data from the PDB which makes it a knowledge-
based approach [32]. Both methods, DSSP and STRIDE, were
reported to have less accuracy to assign π-helix [33]. Many
other computational tools were developed to assign the type of
SSEs for protein residues (i.e, amino acids) when a complete
structure is available and to improve the identification of π-
helix such as SECSTR [34], P-CURVE [35], XTLSSTR [36],
and VoTAP [37].
In many cases, proteins deposited to PDB have missing
atomic data. The number of proteins that have one or more
missing atom information is about 30 − 40% [38]. When
atomic information such as the coordinates of atoms involved
in hydrogen bonds are missing DSSP, STRIDE, and sim-
ilar algorithms become inaccurate and cannot be used. In
addition to experimentally determined structures, structures
produced by computational modeling techniques may not be
complete. Therefore, many tools have been developed to assign
SSEs with missing data. These tools use distance and angle
profiles of local fragments such as the information of Cα
atoms/coordinates in protein’s backbone (i.e., Cα trace). The
first tool to use this approach was proposed in 1977 [39] and
it uses a sliding window that covers four consecutive residues
to find the distances and dihedral angles of Cα coordinates.
Numerous other tools that use Cα coordinates to create a
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profile of geometry based features such as dihedral angles
and Cα distances have been developed following this initial
effort, including P-SEA [40], KAKSI [32], SACF [41], STICK
[42], and PMML [43], and our approach [44]. Recently, some
approaches used machine learning with Cα trace to assign the
SSEs [38], [45].
A. Paper Contributions
• A set of novel geometric features for each Cα using phys-
ical constraints are integrated with additional categorical
features.
• A Deep Neural Network (DNN) is designed and imple-
mented.
In this paper, we develop a deep learning method to assign
the locations of SSEs from a protein’s Cα trace and its
geometry-profile features. The information of other atoms
such as backbone and side chain are not used. Our approach
uses 39 geometric features to assign the types of SSEs. The
rest of paper is organized as follow: Section II describes the
geometric features used in this research. Section III provides
the methodology of this research. Section IV presents the
experimental results and evaluation of the proposed methods
and followed with some conclusions in Section V.
II. F EATURE G ENERATION
In this research, 39 geometric and categorical features are
utilized for each amino acid in the protein’s trace. 26 of those
features are grouped as amino acid distances, atom angles,
vector angles and torsion angles as described in [45] and
depicted in Figure 1. An additional 13 geometric features were
developed (illustrated in Figure 2) and they are also used by
our deep learning system. The vector of 13 features (F α) can
be divided into three (3) category groups: axis distances (Dα),
Euclidean distances (Eα), and Neighborhood (N α). We create
a vector of features (F α) for every individual Cα atom of
the protein that consists of the three (3) category groups of
features. Dα features are the distance between the projection
of the two Cα coordinates of interest on a virtual axis created
using two neighbor Cα coordinates. After creating the virtual
axis, the projections of the two Cα coordinates of interest
are calculated and the distance is found. Eα feature is the
Euclidean distance between the two Cα atoms of interest.
Finally, the N α features are some geometrical and descriptive
features collected for a given Cα atom that describe the
neighborhood of the residue based on some requirements.
The first category of features calculated from Cα coordi-
nates is the set of axis distances, Dα. For residue i, the set of
Dα(i) consists of two axis distances: the distance of residues
i−2 and i−1 on the virtual axis (i.e., line segment) created by
atoms i−2 and i+1 and the distance of residues i and i+1 on
the same virtual axis. The distance in this set is the distance
between the projection of the two Cα atoms of interest on the
virtual axis.
The second category of features calculated from Cα coordi-
nates is the set of Euclidean distances, Eα. Eα(i) consists of
four Euclidean distances of residue i and residues i − 3, i − 2,
 i + 2, and i + 3. The third category of features calculated
from Cα coordinates is the set of geometrical features that
describes the surrounding of Cα atom, N α. N α(i) consists
of four Euclidean distances, two scalar values, and one angular
value for residue i. To calculate this set of features, we initially
find a set of candidate neighbors of residue i. For residue j,
it is considered a candidate neighbor of residue i if all the
following requirements are fulfilled: 1) at least three residues
apart from residue i, |i − j| > 3 2) the distance between i
and j is less than 6.31Å, 3) there is another residue j ′ in
the candidate list that is adjacent to j such that j = j ′ − 1
or j = j ′ + 1. After the initial candidate list of neighbor
residues is created, we drop some weak neighbors based on
the following criterion: for residue j, it is saved in the final
list if the distance of residue j and the line segment formed
between residues i − 1 and i + 1 is less than 5.81Å and its
projection is inside same line segment.
After the final list of neighbors is created, two scalar values
are calculated, the number of neighbors in the list and the
shortest Euclidian distance of residue i and the residues in the
list. Further, we calculate four Euclidean distances between i’s
surrounding and j’s surrounding, where j is the closest residue
in the list to residue i. These distances are distance between
i − 1 and j − 1, the distance between i − 1 and j + 1, the
distance between i + 1 and j − 1, and the distance between
i + 1 and j + 1. Finally, N α(i) contains one angular value,
which is the angle between the vectors formed by i − 1, i + 1
and j − 1, j + 1.
Fig. 1: General geometric features for Cα(i).
III. M ETHOD
Given a problem, there is no universal rule of thumb for
determining the best network architecture that will learn the
solution of that problem. In many cases, it is a hit and miss
kind of a problem. In this study, a systematical approach is
implemented for classification of protein SSE problem. This
approach consists of two network architecture search (NAS)
algorithms each using a different search space. These two NAS
algorithms are used in succession to develop a deep neural
network.
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(a) Two distance features in Dα(i) are
shown in green arrows between the pro-
jection of a Cα coordinates on the virtual
axis.
(b) Four distance features in Eα(i).
(c) Seven features calculated for N α(i).
The final list of neighbors is shown in
green. Two blue Cα residues are candi-
dates removed from the initial list for not
being in accordance with the requirements.
The red lines are four distances calculated
between i’s surrounding and j’s surround-
ing, where j is the closest residue in the
list to i residue.
Fig. 2: The set of geometrical features, F α, collected for each
residue.
A. Dataset
In this study, a dataset of 3946 proteins which consist of
904081 amino acids and their 39 features is used. Among this
dataset, some of the amino acids are removed since they do
not have the features explained in feature generation. With
their removal, the remaining dataset consists of 868027 amino
acids and their 39 features. Out of the 39 features utilized in
this study for SSE classification, one feature corresponds to
the name of the amino acid. Given that there are 20 amino
acids, this name field in the feature vector is replaced with
a one-hot-encoded vector. As a result, for training purposes,
feature vector (input) size of (38+20) is obtained. Similarly, in
this dataset, the SSE elements are divided into three common
structures in proteins α-helices, β-sheets and loops. Hence,
The labels of SSE elements are also one hot encoded into
a label vector with size 3. Then, four different test sets,
each containing 20 unique proteins are subtracted from the
dataset with 3946 proteins. The remaining dataset is divided
into training-validation sets of 90% − 10% amino acid sizes
 respectively. This results in a training set of 766186 amino
acids (approx. 88% of all data), validation set of 85132
(approx. 10% of all data) amino acids and a total test set
of 16708 amino acids (approx. 2% of all data). 37 angle and
distance based features inside sets are standardized ( µ = 0,
σ = 1 ) using the standard deviation and mean obtained from
training set.
B. Network Architecture
In order to build a network architecture, some NAS algo-
rithms are developed. The network architecture is decided by
two different NAS algorithms each using a different search
space. The first algorithm is for selecting network architecture
size and layer connectivity methods. The second algorithm is
for selecting the correct regularization parameters.
Parameters of search space of first stage NAS algorithm
include batch size, number of hidden layers, size of the
layers, and layer types. For layer types, a random selection
between a fully connected layer or a convolutional layer is
used. However, after preliminary experiments, convolutional
layers are excluded from search space and only fully connected
layers are used. Parameters outside of the search space of NAS
algorithm are fixed. All networks picked by NAS algorithm
use ReLU activation other than the last layer, which uses
softmax activation. Furthermore, all networks use ’Adam’
as optimization method and categorical cross-entropy as a
loss function for training. Networks employ a learning rate
scheduler to lower the learning rate at two points of training
(points of 1/3 and 2/3 epochs of total number of epochs). The
purpose of first stage NAS algorithm is to find the network
architecture that maximizes the evaluation measure applied to
the training set predictions using random search. Fig. 3: Graph of resulting network architecture.
Parameters of search space of second stage NAS algorithm
only consists of the ℓ2 regularization weights assigned to
D. Training Method
each layer of the network. Similarly, a learning rate scheduler
is used to lower the learning rate at two points of training Training of the network architecture starts by finding a
(points of 1/3 and 2/3 epochs of total number of epochs). network architecture using first stage NAS algorithm. Then,
The purpose of second stage NAS algorithm is to find the weights of the best network chosen by the first stage NAS are
network architecture that maximizes the evaluation measure transferred to a network with the same architecture, only with
applied to the validation set predictions using grid search. ℓ2 regularization on all layers. Lastly, this network is used as
a base for the second stage NAS algorithm to find a network
C. Evaluation Measures which is regularized in such a way that validation accuracy is
Labeling in such a network is done by highest probability maximized.
label from prediction (output vector). As a consequence, At the first stage of training; learning rates of 10 × 10−2 ,
thresholds are not used in labeling since an amino acid can 3 × 10−2 and 1 × 10−2 are used for 30 epochs each for a total
only have one of the SSE types. For this reason, a basic training of 90 epochs. A network with training accuracy of
understanding of accuracy is used as an evaluation measure. 96.3% and validation accuracy of 91.9% is selected. Selected
Additionally, ROC curves for each label is given individually network shape is a network with increasing width for the first
for comparison of classification consistency of each label. half of layers and getting smaller for the second half of the
1) Accuracy: Classification accuracy is used as the main layers. Neuron counts for each layer of the fully connected
evaluation measure for network performance. Networks are deep network is as follows 58, 228, 290, 399, 379, 225, 123, 3.
compared and selected with their accuracy. Accuracy is de- A diagram of this network can be seen in Figure 3. This
fined as the ratio of correctly assigned labels. network is later used in the second stage of training with
2) ROC curve: ROC curve is calculated by separating the learning rates of 10 × 10−3 , 3 × 10−3 and 1 × 10−3 for 50
output vector into individual labels and predictions. Area under epochs each for a total training of 150 epochs. The selected
ROC curve is also given for comparison reasons. network has a validation accuracy of 93.2%.

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 IV. R ESULTS TABLE III: The performance of our model on the second two
sets of proteins
A network that uses 39 generated geometric and categorical
features is used to correctly label the protein SSEs. The
network architecture decided by NAS algorithms are trained
using 766186 amino acid test set and 85132 amino acid
validation set. This network architecture is described in the
previous section and its architecture can be seen in Figure 3.
Furthermore, this network is tested on four different test sets
of 19 and 20 proteins to label the secondary structure elements
of amino acids inside protein’s trace. The accuracies of this
classifier network can be seen in Table I. Accuracy of the sum
of all test sets is also given in the table as 93.1%. Detailed
information about proteins used in each set and the accuracy
for each protein is shown in Table II and Table III.

Test Set Accuracies

Test Set 1 Test Set 2 Test Set 3 Test Set 4 All Sets
92.9% 92.3% 93.1% 94.1% 93.1%
TABLE I: Test set accuracies for different test sets.

In Figure 4, ROC curves and ROC scores (areas under

ROC curves) are given for each label. All three curves closely
approach the point of a true positive rate of 1 and a false
positive rate of 0. This can be interpreted as the network being
a good classifier. Furthermore, due to the scores of the curves,
it can be said that the labeling performance for helices and
sheets are slightly better than labeling of loops. It can also
be said that the generated features explain helices and sheets
with more certainty.

TABLE II: The performance of our model on the first two sets
of proteins

Fig. 4: Test Set ROC curves for different classes.

V. C ONCLUSIONS

Secondary structures of a protein are used in many structural

bioinformatics applications such as structure comparison and
classification, protein modeling and structure prediction, struc-
ture visualization, protein dynamics, and protein-protein inter-
action. SSEs assignments can be conducted experimentally or
computationally. When experimental methods are unavailable,
computational methods such as DSSP and STRIDE are used
when complete structural information is available for a protein.
When some of the data involved in the calculations to find
the types of SSEs is missing, a reduced representation of a
protein structure can be used to assign the SSEs. The reduced
representation uses the minimum information about protein’s
structure such as Cα trace (i.e., Cα coordinates).
In this paper, we proposed a deep learning method to assign
a type from SSEs to protein’s residues. The approach uses

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 Cα trace of a protein to assign one of three types: helix,
sheet, or loop. It used a set of 39 geometric features for Cα
coordinates for each residue. The model was trained on a data
set of approximately 766K protein residues and validated with
a dataset of approximately 85K residues that were randomly
chosen from cullpdb pc20 res1.8 R0.25 d200528 chains5510.
After training step, the deep learning model was used to assign
a SSE to each residue. The final accuracy of the classifier
was reported for a test set that consists of four groups of
sets conatin either 19 or 20 protein each. When using the
information from PDB as a reference, the classifier model has
achieved accuracy an average accuracy of 93.1% on all test
sets.
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